rs13156086

Variant names:

• chr5-111079771-A-C
• rs13156086
• ENST00000507269.3:n.213-2295T>G

Variant summary

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

The ENST00000507269.3(ENSG00000253613):​n.213-2295T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 152,104 control chromosomes in the GnomAD database, including 5,491 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 0.25 (5491 hom., cov: 32)
• Consequence: ENSG00000253613 ENST00000507269.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.31
• Publications: 5 publications found

Genes affected

ENSG00000253613 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.365 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
ENSG00000253613	ENST00000507269.3	n.213-2295T>G		intron_variant	Intron 2 of 3	5
ENSG00000253613	ENST00000741219.1	n.137-2726T>G		intron_variant	Intron 1 of 2
ENSG00000253613	ENST00000741220.1	n.137-3387T>G		intron_variant	Intron 1 of 1
ENSG00000253613	ENST00000741221.1	n.100-2726T>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.248 AC: 37760 AN: 151986 Hom.: 5490 Cov.: 32

Gnomad AFR AF: 0.0971

Gnomad AMI AF: 0.234

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.379

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.248 AC: 37758 AN: 152104 Hom.: 5491 Cov.: 32 AF XY: 0.255 AC XY: 18921 AN XY: 74338

African (AFR) AF: 0.0968 AC: 4020 AN: 41542

American (AMR) AF: 0.302 AC: 4607 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.361 AC: 1252 AN: 3470

East Asian (EAS) AF: 0.200 AC: 1036 AN: 5178

South Asian (SAS) AF: 0.379 AC: 1829 AN: 4822

European-Finnish (FIN) AF: 0.396 AC: 4172 AN: 10544

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.293 AC: 19941 AN: 67960

Other (OTH) AF: 0.267 AC: 563 AN: 2110

Alfa AF: 0.239 Hom.: 723

Bravo AF: 0.234

Asia WGS AF: 0.276 AC: 961 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	8.2
DANN	Benign	0.35
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs13156086; hg19: chr5-110415469;