chr10-52778780-C-T

Position:

• chr10-52778780-C-T

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;