rs2371208

Variant names:

• chr7-82708543-G-T
• rs2371208

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.474 AC: 19663 AN: 41454

American (AMR) AF: 0.265 AC: 4055 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.184 AC: 639 AN: 3470

East Asian (EAS) AF: 0.426 AC: 2197 AN: 5160

South Asian (SAS) AF: 0.296 AC: 1431 AN: 4830

European-Finnish (FIN) AF: 0.231 AC: 2451 AN: 10594

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.217 AC: 14780 AN: 67972

Other (OTH) AF: 0.268 AC: 566 AN: 2114

Alfa AF: 0.251 Hom.: 14960

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
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs2371208; hg19: chr7-82337859;