rs6708331

Positions:

• chr2-70141791-G-A

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 0.244 in 152,146 control chromosomes in the GnomAD database, including 4,990 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 0.24 (4990 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0150

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.317 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: 0.244 AC: 37078 AN: 152028 Hom.: 4984 Cov.: 33

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.0834

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.244 AC: 37121 AN: 152146 Hom.: 4990 Cov.: 33 AF XY: 0.242 AC XY: 17974 AN XY: 74394

Gnomad4 AFR AF: 0.322

Gnomad4 AMR AF: 0.135

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.112

Gnomad4 SAS AF: 0.0843

Gnomad4 FIN AF: 0.318

Gnomad4 NFE AF: 0.239

Gnomad4 OTH AF: 0.192

Alfa AF: 0.220 Hom.: 6118

Bravo AF: 0.234

Asia WGS AF: 0.128 AC: 442 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	2.5
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6708331; hg19: chr2-70368923;