rs763773

Variant names:

• chr6-144071249-G-T
• rs763773

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 0.394 in 152,046 control chromosomes in the GnomAD database, including 12,764 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 0.39 (12764 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.995

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.556 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: 0.394 AC: 59897 AN: 151928 Hom.: 12748 Cov.: 32

Gnomad AFR AF: 0.562

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.429

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

GnomAD4 genome AF: 0.394 AC: 59949 AN: 152046 Hom.: 12764 Cov.: 32 AF XY: 0.398 AC XY: 29597 AN XY: 74330

Gnomad4 AFR AF: 0.562

Gnomad4 AMR AF: 0.445

Gnomad4 ASJ AF: 0.406

Gnomad4 EAS AF: 0.297

Gnomad4 SAS AF: 0.323

Gnomad4 FIN AF: 0.329

Gnomad4 NFE AF: 0.303

Gnomad4 OTH AF: 0.427

Alfa AF: 0.329 Hom.: 3682

Bravo AF: 0.412

Asia WGS AF: 0.318 AC: 1105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.11
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs763773; hg19: chr6-144392386; COSMIC: COSV60289821;