rs10184004

Variant names:

• chr2-164651879-C-T
• rs10184004

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 0.465 in 151,836 control chromosomes in the GnomAD database, including 18,811 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 0.47 (18811 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.263
• Publications: 35 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.724 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70539 AN: 151718 Hom.: 18762 Cov.: 31

Gnomad AFR AF: 0.730

Gnomad AMI AF: 0.450

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.0890

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.382

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.465 AC: 70631 AN: 151836 Hom.: 18811 Cov.: 31 AF XY: 0.454 AC XY: 33713 AN XY: 74180

African (AFR) AF: 0.731 AC: 30252 AN: 41400

American (AMR) AF: 0.317 AC: 4830 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.356 AC: 1233 AN: 3466

East Asian (EAS) AF: 0.0892 AC: 460 AN: 5158

South Asian (SAS) AF: 0.247 AC: 1190 AN: 4818

European-Finnish (FIN) AF: 0.330 AC: 3480 AN: 10534

Middle Eastern (MID) AF: 0.380 AC: 111 AN: 292

European-Non Finnish (NFE) AF: 0.409 AC: 27792 AN: 67916

Other (OTH) AF: 0.416 AC: 877 AN: 2108

Alfa AF: 0.460 Hom.: 2289

Bravo AF: 0.477

Asia WGS AF: 0.224 AC: 780 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.5
DANN	Benign	0.68
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs10184004; hg19: chr2-165508389;