rs6765491

Variant names:

• chr3-144117848-G-A
• rs6765491

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 0.511 in 151,992 control chromosomes in the GnomAD database, including 23,693 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 0.51 (23693 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.689
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.86 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: 0.511 AC: 77591 AN: 151874 Hom.: 23637 Cov.: 32

Gnomad AFR AF: 0.867

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.354

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.511 AC: 77705 AN: 151992 Hom.: 23693 Cov.: 32 AF XY: 0.509 AC XY: 37844 AN XY: 74298

African (AFR) AF: 0.867 AC: 35986 AN: 41488

American (AMR) AF: 0.463 AC: 7060 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 1393 AN: 3466

East Asian (EAS) AF: 0.442 AC: 2284 AN: 5162

South Asian (SAS) AF: 0.439 AC: 2117 AN: 4824

European-Finnish (FIN) AF: 0.315 AC: 3317 AN: 10546

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.354 AC: 24048 AN: 67942

Other (OTH) AF: 0.491 AC: 1036 AN: 2108

Alfa AF: 0.441 Hom.: 2216

Bravo AF: 0.535

Asia WGS AF: 0.485 AC: 1685 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.2
DANN	Benign	0.48
PhyloP100		0.69

Splicing

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

Other links and lift over

dbSNP: rs6765491; hg19: chr3-143836690;