rs2876666

Positions:

• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;