rs2173201

Variant names:

• chr4-99329813-C-A
• rs2173201

Your query was ambiguous. Multiple possible variants found:

• chr4-99329813-C-A
• chr4-99329813-C-G
• chr4-99329813-C-T

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 0.308 in 152,006 control chromosomes in the GnomAD database, including 8,768 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 0.31 (8768 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.03
• Publications: 14 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 (EAS) allele frequency at 95% confidence interval = 0.734 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: 0.308 AC: 46852 AN: 151888 Hom.: 8770 Cov.: 32

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.220

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.308 AC: 46875 AN: 152006 Hom.: 8768 Cov.: 32 AF XY: 0.314 AC XY: 23311 AN XY: 74282

African (AFR) AF: 0.449 AC: 18603 AN: 41462

American (AMR) AF: 0.212 AC: 3234 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 691 AN: 3472

East Asian (EAS) AF: 0.753 AC: 3897 AN: 5172

South Asian (SAS) AF: 0.534 AC: 2575 AN: 4818

European-Finnish (FIN) AF: 0.165 AC: 1742 AN: 10558

Middle Eastern (MID) AF: 0.223 AC: 65 AN: 292

European-Non Finnish (NFE) AF: 0.224 AC: 15208 AN: 67960

Other (OTH) AF: 0.286 AC: 602 AN: 2106

Alfa AF: 0.247 Hom.: 8098

Bravo AF: 0.311

Asia WGS AF: 0.510 AC: 1773 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	0.20
DANN	Benign	0.45
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs2173201; hg19: chr4-100250970;