chr10-52778780-C-T

Variant names:

• chr10-52778780-C-T
• rs11003136

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 0.361 in 152,046 control chromosomes in the GnomAD database, including 10,104 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 0.36 (10104 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.402 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: 0.361 AC: 54922 AN: 151928 Hom.: 10098 Cov.: 32

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.373

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

GnomAD4 genome AF: 0.361 AC: 54946 AN: 152046 Hom.: 10104 Cov.: 32 AF XY: 0.361 AC XY: 26827 AN XY: 74304

Gnomad4 AFR AF: 0.323

Gnomad4 AMR AF: 0.375

Gnomad4 ASJ AF: 0.448

Gnomad4 EAS AF: 0.320

Gnomad4 SAS AF: 0.417

Gnomad4 FIN AF: 0.341

Gnomad4 NFE AF: 0.378

Gnomad4 OTH AF: 0.369

Alfa AF: 0.321 Hom.: 2616

Bravo AF: 0.361

Asia WGS AF: 0.340 AC: 1182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.2
DANN	Benign	0.91

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11003136; hg19: chr10-54538540; COSMIC: COSV53388008;