chr6-24125860-A-G

Variant names:

• chr6-24125860-A-G
• rs2876666

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 0.327 in 152,062 control chromosomes in the GnomAD database, including 8,481 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 0.33 (8481 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0210
• Publications: 0 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 = 0.583 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: 0.327 AC: 49624 AN: 151942 Hom.: 8467 Cov.: 32

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.600

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.327 AC: 49684 AN: 152062 Hom.: 8481 Cov.: 32 AF XY: 0.327 AC XY: 24263 AN XY: 74304

African (AFR) AF: 0.372 AC: 15433 AN: 41476

American (AMR) AF: 0.287 AC: 4389 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.304 AC: 1056 AN: 3468

East Asian (EAS) AF: 0.601 AC: 3092 AN: 5148

South Asian (SAS) AF: 0.391 AC: 1880 AN: 4814

European-Finnish (FIN) AF: 0.231 AC: 2443 AN: 10584

Middle Eastern (MID) AF: 0.231 AC: 67 AN: 290

European-Non Finnish (NFE) AF: 0.300 AC: 20416 AN: 67978

Other (OTH) AF: 0.323 AC: 680 AN: 2106

Alfa AF: 0.317 Hom.: 1584

Bravo AF: 0.333

Asia WGS AF: 0.476 AC: 1653 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	4.4
DANN	Benign	0.47
PhyloP100		0.021
PromoterAI		-0.011	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2876666; hg19: chr6-24126088;