10-52879340-T-C

Variant names:

• chr10-52879340-T-C
• rs11003238

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 0.313 in 152,124 control chromosomes in the GnomAD database, including 7,565 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 (7565 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.448
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.343 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: 0.313 AC: 47643 AN: 152006 Hom.: 7561 Cov.: 33

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.313 AC: 47670 AN: 152124 Hom.: 7565 Cov.: 33 AF XY: 0.312 AC XY: 23181 AN XY: 74376

African (AFR) AF: 0.262 AC: 10885 AN: 41502

American (AMR) AF: 0.341 AC: 5217 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.306 AC: 1063 AN: 3472

East Asian (EAS) AF: 0.356 AC: 1839 AN: 5162

South Asian (SAS) AF: 0.307 AC: 1482 AN: 4826

European-Finnish (FIN) AF: 0.313 AC: 3311 AN: 10568

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.336 AC: 22827 AN: 67980

Other (OTH) AF: 0.323 AC: 683 AN: 2114

Alfa AF: 0.247 Hom.: 842

Bravo AF: 0.313

Asia WGS AF: 0.303 AC: 1054 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.4
DANN	Benign	0.80
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs11003238; hg19: chr10-54639100;