13-109636620-G-A

Variant names:

• chr13-109636620-G-A
• rs4773068
• ENST00000650264.1:n.759-65462C>T

Variant summary

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

The ENST00000650264.1(ENSG00000285534):​n.759-65462C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0843 in 152,112 control chromosomes in the GnomAD database, including 801 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 0.084 (801 hom., cov: 33)
• Consequence: ENSG00000285534 ENST00000650264.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.954
• Publications: 1 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.291 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.759-65462C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0843 AC: 12806 AN: 151994 Hom.: 795 Cov.: 33

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.0954

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.0591

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0391

Gnomad OTH AF: 0.0910

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

GnomAD4 genome AF: 0.0843 AC: 12830 AN: 152112 Hom.: 801 Cov.: 33 AF XY: 0.0876 AC XY: 6509 AN XY: 74340

African (AFR) AF: 0.112 AC: 4644 AN: 41488

American (AMR) AF: 0.124 AC: 1889 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 447 AN: 3470

East Asian (EAS) AF: 0.303 AC: 1566 AN: 5164

South Asian (SAS) AF: 0.144 AC: 694 AN: 4826

European-Finnish (FIN) AF: 0.0591 AC: 625 AN: 10576

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0391 AC: 2659 AN: 67992

Other (OTH) AF: 0.0919 AC: 194 AN: 2110

Alfa AF: 0.0584 Hom.: 660

Bravo AF: 0.0917

Asia WGS AF: 0.234 AC: 812 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.71
DANN	Benign	0.71
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs4773068; hg19: chr13-110288967;