rs7741751

Variant names:

• chr6-169040845-C-T
• rs7741751

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 0.622 in 152,152 control chromosomes in the GnomAD database, including 29,994 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 0.62 (29994 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0160
• Publications: 5 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 (EAS) allele frequency at 95% confidence interval = 0.735 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: 0.622 AC: 94586 AN: 152034 Hom.: 29982 Cov.: 34

Gnomad AFR AF: 0.711

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.725

Gnomad ASJ AF: 0.557

Gnomad EAS AF: 0.754

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.517

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.680

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

GnomAD4 genome AF: 0.622 AC: 94631 AN: 152152 Hom.: 29994 Cov.: 34 AF XY: 0.619 AC XY: 46032 AN XY: 74366

African (AFR) AF: 0.710 AC: 29473 AN: 41518

American (AMR) AF: 0.725 AC: 11097 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.557 AC: 1934 AN: 3472

East Asian (EAS) AF: 0.754 AC: 3896 AN: 5164

South Asian (SAS) AF: 0.521 AC: 2508 AN: 4818

European-Finnish (FIN) AF: 0.517 AC: 5461 AN: 10568

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.561 AC: 38173 AN: 67994

Other (OTH) AF: 0.682 AC: 1441 AN: 2112

Alfa AF: 0.609 Hom.: 5001

Bravo AF: 0.642

Asia WGS AF: 0.665 AC: 2314 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	1.0
DANN	Benign	0.78
PhyloP100		-0.016

Splicing

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

Other links and lift over

dbSNP: rs7741751; hg19: chr6-169440940; COSMIC: COSV60305421;