10-13234751-G-C

Position:

• chr10-13234751-G-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 0.0997 in 152,168 control chromosomes in the GnomAD database, including 981 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 0.10 (981 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.125

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.216 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: 0.0998 AC: 15178 AN: 152050 Hom.: 981 Cov.: 30

Gnomad AFR AF: 0.0246

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.0705

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.0997 AC: 15170 AN: 152168 Hom.: 981 Cov.: 30 AF XY: 0.0995 AC XY: 7399 AN XY: 74388

Gnomad4 AFR AF: 0.0245

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.189

Gnomad4 EAS AF: 0.227

Gnomad4 SAS AF: 0.164

Gnomad4 FIN AF: 0.0705

Gnomad4 NFE AF: 0.126

Gnomad4 OTH AF: 0.129

Alfa AF: 0.0525 Hom.: 38

Bravo AF: 0.0989

Asia WGS AF: 0.181 AC: 630 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.6
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17152980; hg19: chr10-13276751;