rs6765337

Positions:

• chr3-176939674-T-C

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 0.0916 in 152,284 control chromosomes in the GnomAD database, including 734 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 0.092 (734 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.647

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.133 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: 0.0916 AC: 13933 AN: 152166 Hom.: 733 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0731

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.0673

Gnomad SAS AF: 0.0586

Gnomad FIN AF: 0.0585

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.0772

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.0916 AC: 13949 AN: 152284 Hom.: 734 Cov.: 32 AF XY: 0.0891 AC XY: 6632 AN XY: 74462

Gnomad4 AFR AF: 0.136

Gnomad4 AMR AF: 0.0729

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.0671

Gnomad4 SAS AF: 0.0588

Gnomad4 FIN AF: 0.0585

Gnomad4 NFE AF: 0.0772

Gnomad4 OTH AF: 0.104

Alfa AF: 0.0801 Hom.: 257

Bravo AF: 0.0956

Asia WGS AF: 0.0680 AC: 235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.2
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6765337; hg19: chr3-176657462;