rs6740847

Positions:

• chr2-181443625-A-G

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 0.57 in 151,846 control chromosomes in the GnomAD database, including 25,304 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 0.57 (25304 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.249

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.629 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.570 AC: 86549 AN: 151728 Hom.: 25283 Cov.: 32

Gnomad AFR AF: 0.636

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.489

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.622

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.559

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

GnomAD4 genome AF: 0.570 AC: 86608 AN: 151846 Hom.: 25304 Cov.: 32 AF XY: 0.572 AC XY: 42425 AN XY: 74184

Gnomad4 AFR AF: 0.636

Gnomad4 AMR AF: 0.499

Gnomad4 ASJ AF: 0.489

Gnomad4 EAS AF: 0.332

Gnomad4 SAS AF: 0.613

Gnomad4 FIN AF: 0.622

Gnomad4 NFE AF: 0.558

Gnomad4 OTH AF: 0.553

Alfa AF: 0.551 Hom.: 46972

Bravo AF: 0.562

Asia WGS AF: 0.472 AC: 1637 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6740847; hg19: chr2-182308352;