rs12865636

Variant names:

• chr13-109647577-G-A
• rs12865636
• ENST00000650264.1:n.759-76419C>T

Your query was ambiguous. Multiple possible variants found:

• chr13-109647577-G-A
• chr13-109647577-G-T

Variant summary

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

The ENST00000650264.1(ENSG00000285534):​n.759-76419C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0895 in 152,130 control chromosomes in the GnomAD database, including 671 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 0.089 (671 hom., cov: 31)
• Consequence: ENSG00000285534 ENST00000650264.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16
• Publications: 3 publications found

Genes affected

ENSG00000285534 (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 = 0.0965 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
ENSG00000285534	ENST00000650264.1	n.759-76419C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0895 AC: 13600 AN: 152012 Hom.: 666 Cov.: 31

Gnomad AFR AF: 0.0989

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.0769

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.0112

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.0362

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0978

Gnomad OTH AF: 0.0951

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

GnomAD4 genome AF: 0.0895 AC: 13614 AN: 152130 Hom.: 671 Cov.: 31 AF XY: 0.0862 AC XY: 6407 AN XY: 74366

African (AFR) AF: 0.0990 AC: 4109 AN: 41496

American (AMR) AF: 0.0767 AC: 1173 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.128 AC: 444 AN: 3468

East Asian (EAS) AF: 0.0112 AC: 58 AN: 5172

South Asian (SAS) AF: 0.104 AC: 502 AN: 4826

European-Finnish (FIN) AF: 0.0362 AC: 383 AN: 10572

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0978 AC: 6648 AN: 67990

Other (OTH) AF: 0.0941 AC: 198 AN: 2104

Alfa AF: 0.0927 Hom.: 873

Bravo AF: 0.0896

Asia WGS AF: 0.0550 AC: 192 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.29
DANN	Benign	0.14
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs12865636; hg19: chr13-110299924;