rs10184004

Variant names:

• chr2-164651879-C-T
• rs10184004

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.465 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

Gnomad4 AFR AF: 0.731

Gnomad4 AMR AF: 0.317

Gnomad4 ASJ AF: 0.356

Gnomad4 EAS AF: 0.0892

Gnomad4 SAS AF: 0.247

Gnomad4 FIN AF: 0.330

Gnomad4 NFE AF: 0.409

Gnomad4 OTH AF: 0.416

Alfa AF: 0.450 Hom.: 2095

Bravo AF: 0.477

Asia WGS AF: 0.224 AC: 780 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10184004; hg19: chr2-165508389;