rs10507756

Positions:

• chr13-68907470-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 0.124 in 152,222 control chromosomes in the GnomAD database, including 1,596 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 0.12 (1596 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.916

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.177 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: 0.124 AC: 18832 AN: 152104 Hom.: 1595 Cov.: 32

Gnomad AFR AF: 0.0336

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0856

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.194

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.124 AC: 18835 AN: 152222 Hom.: 1596 Cov.: 32 AF XY: 0.120 AC XY: 8954 AN XY: 74414

Gnomad4 AFR AF: 0.0337

Gnomad4 AMR AF: 0.134

Gnomad4 ASJ AF: 0.257

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.0861

Gnomad4 FIN AF: 0.131

Gnomad4 NFE AF: 0.179

Gnomad4 OTH AF: 0.148

Alfa AF: 0.145 Hom.: 242

Bravo AF: 0.122

Asia WGS AF: 0.0480 AC: 168 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.73
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10507756; hg19: chr13-69481602;