rs977102

Positions:

• chr3-67323553-A-G

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;