10-13268071-T-C

Position:

• chr10-13268071-T-C

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 0.346 in 151,838 control chromosomes in the GnomAD database, including 10,935 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 0.35 (10935 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.447 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.346 AC: 52534 AN: 151722 Hom.: 10932 Cov.: 31

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.448

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.346 AC: 52536 AN: 151838 Hom.: 10935 Cov.: 31 AF XY: 0.347 AC XY: 25710 AN XY: 74194

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.456

Gnomad4 ASJ AF: 0.394

Gnomad4 EAS AF: 0.400

Gnomad4 SAS AF: 0.406

Gnomad4 FIN AF: 0.397

Gnomad4 NFE AF: 0.448

Gnomad4 OTH AF: 0.365

Alfa AF: 0.432 Hom.: 29259

Bravo AF: 0.340

Asia WGS AF: 0.364 AC: 1267 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.8
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10796051; hg19: chr10-13310071;