rs2161

Variant names:

• chr7-98463194-G-A
• rs2161

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.367 in 151,998 control chromosomes in the GnomAD database, including 10,771 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 0.37 (10771 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.153
• Publications: 14 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.19).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.548 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: 0.367 AC: 55681 AN: 151880 Hom.: 10755 Cov.: 32

Gnomad AFR AF: 0.450

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.565

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.367 AC: 55738 AN: 151998 Hom.: 10771 Cov.: 32 AF XY: 0.372 AC XY: 27615 AN XY: 74286

African (AFR) AF: 0.450 AC: 18632 AN: 41436

American (AMR) AF: 0.383 AC: 5847 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 799 AN: 3470

East Asian (EAS) AF: 0.565 AC: 2916 AN: 5158

South Asian (SAS) AF: 0.339 AC: 1632 AN: 4818

European-Finnish (FIN) AF: 0.412 AC: 4352 AN: 10560

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.300 AC: 20399 AN: 67972

Other (OTH) AF: 0.333 AC: 703 AN: 2112

Alfa AF: 0.316 Hom.: 25419

Bravo AF: 0.370

Asia WGS AF: 0.450 AC: 1568 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.19
CADD	Benign	18
DANN	Benign	0.77
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs2161; hg19: chr7-98092506; COSMIC: COSV62496727;