chr6-24646593-C-T

Variant names:

• chr6-24646593-C-T
• rs3756821

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 0.415 in 152,026 control chromosomes in the GnomAD database, including 13,377 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 (13377 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.858
• Publications: 20 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.457 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: 0.415 AC: 63110 AN: 151908 Hom.: 13371 Cov.: 32

Gnomad AFR AF: 0.464

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.415 AC: 63139 AN: 152026 Hom.: 13377 Cov.: 32 AF XY: 0.407 AC XY: 30265 AN XY: 74316

African (AFR) AF: 0.463 AC: 19182 AN: 41436

American (AMR) AF: 0.351 AC: 5362 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.387 AC: 1342 AN: 3468

East Asian (EAS) AF: 0.241 AC: 1240 AN: 5154

South Asian (SAS) AF: 0.249 AC: 1199 AN: 4818

European-Finnish (FIN) AF: 0.368 AC: 3896 AN: 10582

Middle Eastern (MID) AF: 0.435 AC: 127 AN: 292

European-Non Finnish (NFE) AF: 0.435 AC: 29539 AN: 67976

Other (OTH) AF: 0.409 AC: 863 AN: 2108

Alfa AF: 0.429 Hom.: 22599

Bravo AF: 0.419

Asia WGS AF: 0.264 AC: 919 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.74
PhyloP100		-0.86
PromoterAI		-0.0058	Neutral

Splicing

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

Other links and lift over

dbSNP: rs3756821; hg19: chr6-24646821;