dbSNP rs8100455: ZNF331:c.-323C>G (chr19-53522034-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000253144.13(ZNF331):c.-323C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.321 in 151,902 control chromosomes in the GnomAD database, including 8,000 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 0.32 ( 8000 hom., cov: 31)

Exomes 𝑓: 0.33 ( 0 hom. )

Consequence

ZNF331
ENST00000253144.13 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.546

Publications

7 publications found

Variant links:

Genes affected

ZNF331 (HGNC:15489): (zinc finger protein 331) This gene encodes a zinc finger protein containing a KRAB (Kruppel-associated box) domain found in transcriptional repressors. This gene may be methylated and silenced in cancer cells. This gene is located within a differentially methylated region (DMR) and shows allele-specific expression in placenta. Alternative splicing and the use of alternative promoters results in multiple transcript variants encoding the same protein. [provided by RefSeq, Nov 2015]

ZNF331 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=-0.88).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	Protein	UniProt
ZNF331	NM_001317120.2 link	c.-285C>G	5_prime_UTR_variant	Exon 1 of 7	NP_001304049.1	Q9NQX6A0A024R4J5Q71QC4Q68D63
ZNF331	NM_018555.6 link	c.-323C>G	5_prime_UTR_variant	Exon 1 of 7	NP_061025.5	Q9NQX6A0A024R4J5Q68D63
ZNF331	XM_011527076.4 link	c.-754C>G	5_prime_UTR_variant	Exon 1 of 8	XP_011525378.1	Q9NQX6A0A024R4J5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	Protein	UniProt
ZNF331	ENST00000253144.13 link	c.-323C>G	5_prime_UTR_variant	Exon 1 of 7	1	ENSP00000253144.9	Q9NQX6
ZNF331	ENST00000502248.5 link	c.-285C>G	5_prime_UTR_variant	Exon 1 of 7	1	ENSP00000423675.1	E7EV14
ZNF331	ENST00000513929.6 link	n.1052C>G	non_coding_transcript_exon_variant	Exon 1 of 3	2

Frequencies

GnomAD3 genomes

AF:

0.322

AC:

48792

AN:

151760

Hom.:

7997

Cov.:

show subpopulations

Gnomad AFR

AF:

0.350

Gnomad AMI

AF:

0.242

Gnomad AMR

AF:

0.317

Gnomad ASJ

AF:

0.414

Gnomad EAS

AF:

0.194

Gnomad SAS

AF:

0.388

Gnomad FIN

AF:

0.288

Gnomad MID

AF:

0.430

Gnomad NFE

AF:

0.311

Gnomad OTH

AF:

0.348

GnomAD4 exome

AF:

0.333

AC:

AN:

Hom.:

Cov.:

AF XY:

0.389

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.500

AC:

AN:

European-Finnish (FIN)

AF:

0.250

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.333

AC:

AN:

Other (OTH)

AF:

0.375

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.556

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:

0.321

AC:

48806

AN:

151878

Hom.:

8000

Cov.:

AF XY:

0.322

AC XY:

23899

AN XY:

74236

show subpopulations

African (AFR)

AF:

0.349

AC:

14450

AN:

41374

American (AMR)

AF:

0.316

AC:

4831

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.414

AC:

1434

AN:

3466

East Asian (EAS)

AF:

0.194

AC:

992

AN:

5126

South Asian (SAS)

AF:

0.389

AC:

1873

AN:

4818

European-Finnish (FIN)

AF:

0.288

AC:

3040

AN:

10548

Middle Eastern (MID)

AF:

0.418

AC:

122

AN:

292

European-Non Finnish (NFE)

AF:

0.311

AC:

21112

AN:

67964

Other (OTH)

AF:

0.348

AC:

732

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1681

3363

5044

6726

8407

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

502

1004

1506

2008

2510

<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:

0.301

Hom.:

912

Bravo

AF:

0.328

Asia WGS

AF:

0.283

AC:

983

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

2.4

(source)

DANN

Benign

0.48

PhyloP100

-0.55

PromoterAI

-0.020

Neutral

(source)

Mutation Taster

=300/0

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over