rs977102

Variant names:

• chr3-67323553-A-G
• rs977102

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.0950

Gnomad4 AMR AF: 0.122

Gnomad4 ASJ AF: 0.217

Gnomad4 EAS AF: 0.165

Gnomad4 SAS AF: 0.0698

Gnomad4 FIN AF: 0.0620

Gnomad4 NFE AF: 0.122

Gnomad4 OTH AF: 0.150

Alfa AF: 0.120 Hom.: 579

Bravo AF: 0.118

Asia WGS AF: 0.119 AC: 416 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs977102; hg19: chr3-67373977;