rs2844621

Positions:

• chr6-31273760-C-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 0.742 in 152,084 control chromosomes in the GnomAD database, including 41,974 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 0.74 (41974 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.653

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.78 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: 0.742 AC: 112716 AN: 151968 Hom.: 41924 Cov.: 32

Gnomad AFR AF: 0.751

Gnomad AMI AF: 0.721

Gnomad AMR AF: 0.745

Gnomad ASJ AF: 0.791

Gnomad EAS AF: 0.726

Gnomad SAS AF: 0.801

Gnomad FIN AF: 0.795

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.721

Gnomad OTH AF: 0.752

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

GnomAD4 genome AF: 0.742 AC: 112824 AN: 152084 Hom.: 41974 Cov.: 32 AF XY: 0.748 AC XY: 55614 AN XY: 74356

Gnomad4 AFR AF: 0.751

Gnomad4 AMR AF: 0.745

Gnomad4 ASJ AF: 0.791

Gnomad4 EAS AF: 0.727

Gnomad4 SAS AF: 0.801

Gnomad4 FIN AF: 0.795

Gnomad4 NFE AF: 0.721

Gnomad4 OTH AF: 0.752

Alfa AF: 0.726 Hom.: 3704

Bravo AF: 0.738

Asia WGS AF: 0.782 AC: 2717 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.6
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2844621; hg19: chr6-31241537;