dbSNP rs12971799: ZNF665:c.*580A>G (chr19-53163873-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_024733.5(ZNF665):c.*580A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.516 in 152,084 control chromosomes in the GnomAD database, including 22,966 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 0.52 ( 22963 hom., cov: 32)

Exomes 𝑓: 0.42 ( 3 hom. )

Consequence

ZNF665
NM_024733.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.70

Publications

3 publications found

Variant links:

Genes affected

ZNF665 (HGNC:25885): (zinc finger protein 665) 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]

ZNF665 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=-0.9).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024733.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ZNF665	NM_024733.5	MANE Select	c.*580A>G	3_prime_UTR	Exon 4 of 4	NP_079009.3
ZNF665	NM_001353458.2		c.*580A>G	3_prime_UTR	Exon 5 of 5	NP_001340387.1
ZNF665	NM_001353459.2		c.*580A>G	3_prime_UTR	Exon 4 of 4	NP_001340388.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF665	ENST00000396424.5	TSL:2 MANE Select	c.*580A>G		3_prime_UTR	Exon 4 of 4	ENSP00000379702.2
	ZNF665	ENST00000596564.1	TSL:5	n.27A>G		non_coding_transcript_exon	Exon 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.516

AC:

78455

AN:

151912

Hom.:

22950

Cov.:

show subpopulations

Gnomad AFR

AF:

0.230

Gnomad AMI

AF:

0.630

Gnomad AMR

AF:

0.615

Gnomad ASJ

AF:

0.508

Gnomad EAS

AF:

0.656

Gnomad SAS

AF:

0.715

Gnomad FIN

AF:

0.667

Gnomad MID

AF:

0.459

Gnomad NFE

AF:

0.620

Gnomad OTH

AF:

0.519

GnomAD4 exome

AF:

0.423

AC:

AN:

Hom.:

Cov.:

AF XY:

0.441

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.409

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.516

AC:

78498

AN:

152032

Hom.:

22963

Cov.:

AF XY:

0.524

AC XY:

38941

AN XY:

74308

show subpopulations

African (AFR)

AF:

0.230

AC:

9529

AN:

41504

American (AMR)

AF:

0.616

AC:

9390

AN:

15246

Ashkenazi Jewish (ASJ)

AF:

0.508

AC:

1762

AN:

3468

East Asian (EAS)

AF:

0.657

AC:

3378

AN:

5144

South Asian (SAS)

AF:

0.715

AC:

3452

AN:

4830

European-Finnish (FIN)

AF:

0.667

AC:

7043

AN:

10564

Middle Eastern (MID)

AF:

0.456

AC:

134

AN:

294

European-Non Finnish (NFE)

AF:

0.620

AC:

42142

AN:

67968

Other (OTH)

AF:

0.520

AC:

1095

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1671

3342

5014

6685

8356

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

684

1368

2052

2736

3420

<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:

0.550

Hom.:

18315

Bravo

AF:

0.497

Asia WGS

AF:

0.653

AC:

2272

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

4.4

(source)

DANN

Benign

0.57

PhyloP100

-1.7

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