6-144071249-G-T

Variant names:

• chr6-144071249-G-T
• rs763773

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 0.394 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.562 AC: 23282 AN: 41446

American (AMR) AF: 0.445 AC: 6797 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.406 AC: 1407 AN: 3468

East Asian (EAS) AF: 0.297 AC: 1538 AN: 5180

South Asian (SAS) AF: 0.323 AC: 1555 AN: 4820

European-Finnish (FIN) AF: 0.329 AC: 3478 AN: 10568

Middle Eastern (MID) AF: 0.438 AC: 128 AN: 292

European-Non Finnish (NFE) AF: 0.303 AC: 20629 AN: 67984

Other (OTH) AF: 0.427 AC: 900 AN: 2110

Alfa AF: 0.328 Hom.: 4108

Bravo AF: 0.412

Asia WGS AF: 0.318 AC: 1105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.11
DANN	Benign	0.26
PhyloP100		-0.99

Splicing

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

Other links and lift over

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