rs2371208

Positions:

• chr7-82708543-G-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 0.303 in 152,076 control chromosomes in the GnomAD database, including 8,010 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 0.30 (8010 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.116

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 (AFR) allele frequency at 95% confidence interval = 0.469 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: 0.303 AC: 46023 AN: 151958 Hom.: 7986 Cov.: 32

Gnomad AFR AF: 0.474

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.303 AC: 46083 AN: 152076 Hom.: 8010 Cov.: 32 AF XY: 0.305 AC XY: 22661 AN XY: 74360

Gnomad4 AFR AF: 0.474

Gnomad4 AMR AF: 0.265

Gnomad4 ASJ AF: 0.184

Gnomad4 EAS AF: 0.426

Gnomad4 SAS AF: 0.296

Gnomad4 FIN AF: 0.231

Gnomad4 NFE AF: 0.217

Gnomad4 OTH AF: 0.268

Alfa AF: 0.230 Hom.: 7608

Bravo AF: 0.310

Asia WGS AF: 0.333 AC: 1160 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	1.8
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2371208; hg19: chr7-82337859;