13-47395940-G-A

Variant names:

• chr13-47395940-G-A
• rs10507556
• ENST00000751481.1:n.158+23193C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000751481.1(ENSG00000297874):​n.158+23193C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 151,966 control chromosomes in the GnomAD database, including 4,131 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 0.20 (4131 hom., cov: 32)
• Consequence: ENSG00000297874 ENST00000751481.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.197
• Publications: 3 publications found

Genes affected

ENSG00000297874 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.388 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
ENSG00000297874	ENST00000751481.1	n.158+23193C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30239 AN: 151848 Hom.: 4123 Cov.: 32

Gnomad AFR AF: 0.393

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.0448

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.199 AC: 30277 AN: 151966 Hom.: 4131 Cov.: 32 AF XY: 0.197 AC XY: 14617 AN XY: 74258

African (AFR) AF: 0.393 AC: 16273 AN: 41444

American (AMR) AF: 0.163 AC: 2482 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.153 AC: 532 AN: 3468

East Asian (EAS) AF: 0.0449 AC: 232 AN: 5166

South Asian (SAS) AF: 0.182 AC: 876 AN: 4822

European-Finnish (FIN) AF: 0.106 AC: 1124 AN: 10554

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.121 AC: 8252 AN: 67932

Other (OTH) AF: 0.188 AC: 396 AN: 2110

Alfa AF: 0.128 Hom.: 852

Bravo AF: 0.210

Asia WGS AF: 0.147 AC: 510 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.80
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs10507556; hg19: chr13-47970075;