chr6-151624531-C-T

Variant names:

• chr6-151624531-C-T
• rs7776340

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 0.501 in 151,848 control chromosomes in the GnomAD database, including 19,366 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 0.50 (19366 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.125
• Publications: 12 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 = 0.54 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: 0.501 AC: 76072 AN: 151732 Hom.: 19345 Cov.: 32

Gnomad AFR AF: 0.546

Gnomad AMI AF: 0.347

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.580

Gnomad NFE AF: 0.510

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.501 AC: 76133 AN: 151848 Hom.: 19366 Cov.: 32 AF XY: 0.495 AC XY: 36768 AN XY: 74218

African (AFR) AF: 0.546 AC: 22602 AN: 41396

American (AMR) AF: 0.398 AC: 6076 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.553 AC: 1919 AN: 3468

East Asian (EAS) AF: 0.412 AC: 2124 AN: 5158

South Asian (SAS) AF: 0.514 AC: 2475 AN: 4814

European-Finnish (FIN) AF: 0.449 AC: 4738 AN: 10562

Middle Eastern (MID) AF: 0.586 AC: 171 AN: 292

European-Non Finnish (NFE) AF: 0.510 AC: 34624 AN: 67884

Other (OTH) AF: 0.516 AC: 1088 AN: 2110

Alfa AF: 0.507 Hom.: 10284

Bravo AF: 0.499

Asia WGS AF: 0.486 AC: 1691 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.4
DANN	Benign	0.51
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs7776340; hg19: chr6-151945666;