rs2171493

Variant names:

• chr7-130266307-A-C
• rs2171493

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 0.204 in 152,196 control chromosomes in the GnomAD database, including 3,555 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 0.20 (3555 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.254
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.246 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: 0.204 AC: 31078 AN: 152078 Hom.: 3553 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.0156

Gnomad SAS AF: 0.0734

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.204 AC: 31084 AN: 152196 Hom.: 3555 Cov.: 32 AF XY: 0.198 AC XY: 14706 AN XY: 74398

African (AFR) AF: 0.176 AC: 7304 AN: 41540

American (AMR) AF: 0.179 AC: 2738 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.297 AC: 1030 AN: 3468

East Asian (EAS) AF: 0.0154 AC: 80 AN: 5190

South Asian (SAS) AF: 0.0720 AC: 347 AN: 4822

European-Finnish (FIN) AF: 0.179 AC: 1892 AN: 10588

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.249 AC: 16937 AN: 67976

Other (OTH) AF: 0.215 AC: 455 AN: 2116

Alfa AF: 0.240 Hom.: 10846

Bravo AF: 0.205

Asia WGS AF: 0.0550 AC: 192 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	12
DANN	Benign	0.54
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs2171493; hg19: chr7-129906147;