13-68907470-G-C

Variant names:

• chr13-68907470-G-C
• rs10507756

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.0337 AC: 1399 AN: 41554

American (AMR) AF: 0.134 AC: 2040 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 891 AN: 3470

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5182

South Asian (SAS) AF: 0.0861 AC: 416 AN: 4832

European-Finnish (FIN) AF: 0.131 AC: 1390 AN: 10594

Middle Eastern (MID) AF: 0.199 AC: 58 AN: 292

European-Non Finnish (NFE) AF: 0.179 AC: 12189 AN: 67994

Other (OTH) AF: 0.148 AC: 313 AN: 2114

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
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs10507756; hg19: chr13-69481602;