dbSNP rs7247513: ZNF490:c.*114G>A (chr19-12580371-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_020714.3(ZNF490):c.*114G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.641 in 1,478,468 control chromosomes in the GnomAD database, including 313,605 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.58 ( 26582 hom., cov: 32)

Exomes 𝑓: 0.65 ( 287023 hom. )

Consequence

ZNF490
NM_020714.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.24

Publications

23 publications found

Variant links:

Genes affected

ZNF490 (HGNC:23705): (zinc finger protein 490) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZNF490 links:

ENSG00000269693 (HGNC:):

ENSG00000269693 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.683 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020714.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF490	NM_020714.3	MANE Select	c.*114G>A		3_prime_UTR	Exon 5 of 5	NP_065765.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ZNF490	ENST00000311437.11	TSL:1 MANE Select	c.*114G>A	3_prime_UTR	Exon 5 of 5	ENSP00000311521.6
ENSG00000269693	ENST00000593682.1	TSL:1	n.*114G>A	non_coding_transcript_exon	Exon 1 of 4	ENSP00000473043.1
ENSG00000269693	ENST00000593682.1	TSL:1	n.*114G>A	3_prime_UTR	Exon 1 of 4	ENSP00000473043.1

Frequencies

GnomAD3 genomes

AF:

0.575

AC:

87397

AN:

151896

Hom.:

26559

Cov.:

show subpopulations

Gnomad AFR

AF:

0.443

Gnomad AMI

AF:

0.628

Gnomad AMR

AF:

0.528

Gnomad ASJ

AF:

0.768

Gnomad EAS

AF:

0.169

Gnomad SAS

AF:

0.429

Gnomad FIN

AF:

0.620

Gnomad MID

AF:

0.617

Gnomad NFE

AF:

0.689

Gnomad OTH

AF:

0.607

GnomAD4 exome

AF:

0.649

AC:

860306

AN:

1326454

Hom.:

287023

Cov.:

AF XY:

0.645

AC XY:

417646

AN XY:

647238

show subpopulations

African (AFR)

AF:

0.423

AC:

12653

AN:

29884

American (AMR)

AF:

0.496

AC:

13669

AN:

27584

Ashkenazi Jewish (ASJ)

AF:

0.777

AC:

14975

AN:

19278

East Asian (EAS)

AF:

0.216

AC:

8333

AN:

38602

South Asian (SAS)

AF:

0.438

AC:

26907

AN:

61428

European-Finnish (FIN)

AF:

0.627

AC:

25052

AN:

39970

Middle Eastern (MID)

AF:

0.673

AC:

2585

AN:

3842

European-Non Finnish (NFE)

AF:

0.687

AC:

722255

AN:

1051060

Other (OTH)

AF:

0.618

AC:

33877

AN:

54806

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.486

Heterozygous variant carriers

14836

29672

44508

59344

74180

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

18994

37988

56982

75976

94970

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.575

AC:

87460

AN:

152014

Hom.:

26582

Cov.:

AF XY:

0.565

AC XY:

41973

AN XY:

74310

show subpopulations

African (AFR)

AF:

0.443

AC:

18374

AN:

41440

American (AMR)

AF:

0.528

AC:

8063

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.768

AC:

2664

AN:

3468

East Asian (EAS)

AF:

0.169

AC:

874

AN:

5166

South Asian (SAS)

AF:

0.429

AC:

2069

AN:

4820

European-Finnish (FIN)

AF:

0.620

AC:

6557

AN:

10568

Middle Eastern (MID)

AF:

0.626

AC:

184

AN:

294

European-Non Finnish (NFE)

AF:

0.689

AC:

46814

AN:

67972

Other (OTH)

AF:

0.612

AC:

1288

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1801

3602

5403

7204

9005

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

726

1452

2178

2904

3630

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.647

Hom.:

135650

Bravo

AF:

0.563

Asia WGS

AF:

0.327

AC:

1143

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

1.2

(source)

DANN

Benign

0.88

PhyloP100

-4.2

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over