rs10171238

Variant names:

• chr2-148811160-C-T
• rs10171238

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 0.618 in 152,030 control chromosomes in the GnomAD database, including 32,118 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 0.62 (32118 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.44
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.773 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.618 AC: 93935 AN: 151912 Hom.: 32130 Cov.: 32

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.796

Gnomad AMR AF: 0.661

Gnomad ASJ AF: 0.717

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.743

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.778

Gnomad OTH AF: 0.647

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

GnomAD4 genome AF: 0.618 AC: 93928 AN: 152030 Hom.: 32118 Cov.: 32 AF XY: 0.614 AC XY: 45608 AN XY: 74308

African (AFR) AF: 0.364 AC: 15096 AN: 41430

American (AMR) AF: 0.660 AC: 10097 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.717 AC: 2486 AN: 3466

East Asian (EAS) AF: 0.176 AC: 908 AN: 5164

South Asian (SAS) AF: 0.473 AC: 2279 AN: 4818

European-Finnish (FIN) AF: 0.743 AC: 7851 AN: 10564

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.778 AC: 52913 AN: 67976

Other (OTH) AF: 0.640 AC: 1351 AN: 2110

Alfa AF: 0.713 Hom.: 122220

Bravo AF: 0.596

Asia WGS AF: 0.317 AC: 1107 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	11
DANN	Benign	0.79
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs10171238; hg19: chr2-149568729;