6-155746739-G-A

Variant names:

• chr6-155746739-G-A
• rs716435

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 0.423 in 151,942 control chromosomes in the GnomAD database, including 13,821 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 0.42 (13821 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.15
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.471 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.423 AC: 64273 AN: 151826 Hom.: 13808 Cov.: 33

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.463

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.423 AC: 64298 AN: 151942 Hom.: 13821 Cov.: 33 AF XY: 0.430 AC XY: 31918 AN XY: 74264

African (AFR) AF: 0.365 AC: 15128 AN: 41440

American (AMR) AF: 0.480 AC: 7324 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.463 AC: 1608 AN: 3470

East Asian (EAS) AF: 0.399 AC: 2062 AN: 5164

South Asian (SAS) AF: 0.460 AC: 2218 AN: 4822

European-Finnish (FIN) AF: 0.540 AC: 5684 AN: 10530

Middle Eastern (MID) AF: 0.366 AC: 106 AN: 290

European-Non Finnish (NFE) AF: 0.425 AC: 28848 AN: 67948

Other (OTH) AF: 0.416 AC: 877 AN: 2110

Alfa AF: 0.383 Hom.: 3407

Bravo AF: 0.415

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.0060
DANN	Benign	0.56
PhyloP100		-3.1

Splicing

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

Other links and lift over

dbSNP: rs716435; hg19: chr6-156067873; COSMIC: COSV60295220;