rs977102

Variant names:

• chr3-67323553-A-G
• rs977102

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.113 in 152,046 control chromosomes in the GnomAD database, including 1,044 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 0.11 (1044 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.125
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.156 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17194 AN: 151928 Hom.: 1049 Cov.: 31

Gnomad AFR AF: 0.0950

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.0699

Gnomad FIN AF: 0.0620

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.153

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.113 AC: 17177 AN: 152046 Hom.: 1044 Cov.: 31 AF XY: 0.110 AC XY: 8180 AN XY: 74310

African (AFR) AF: 0.0950 AC: 3939 AN: 41480

American (AMR) AF: 0.122 AC: 1859 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.217 AC: 754 AN: 3470

East Asian (EAS) AF: 0.165 AC: 851 AN: 5150

South Asian (SAS) AF: 0.0698 AC: 336 AN: 4814

European-Finnish (FIN) AF: 0.0620 AC: 656 AN: 10580

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.122 AC: 8276 AN: 67980

Other (OTH) AF: 0.150 AC: 315 AN: 2104

Alfa AF: 0.121 Hom.: 2223

Bravo AF: 0.118

Asia WGS AF: 0.119 AC: 416 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.9
DANN	Benign	0.91
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs977102; hg19: chr3-67373977;