rs2876666

Variant names:

• chr6-24125860-A-G
• rs2876666

Your query was ambiguous. Multiple possible variants found:

• chr6-24125860-A-G
• chr6-24125860-A-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.372

Gnomad4 AMR AF: 0.287

Gnomad4 ASJ AF: 0.304

Gnomad4 EAS AF: 0.601

Gnomad4 SAS AF: 0.391

Gnomad4 FIN AF: 0.231

Gnomad4 NFE AF: 0.300

Gnomad4 OTH AF: 0.323

Alfa AF: 0.315 Hom.: 1520

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2876666; hg19: chr6-24126088;