13-94982059-T-C

Variant names:

• chr13-94982059-T-C
• rs2148065
• ENST00000669430.1:n.73-20280A>G

Variant summary

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

The ENST00000669430.1(ENSG00000287635):​n.73-20280A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.893 in 152,200 control chromosomes in the GnomAD database, including 62,478 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 0.89 (62478 hom., cov: 32)
• Consequence: ENSG00000287635 ENST00000669430.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0950
• Publications: 3 publications found

Genes affected

ENSG00000287635 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.99 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
ENSG00000287635	ENST00000669430.1	n.73-20280A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.894 AC: 135923 AN: 152082 Hom.: 62462 Cov.: 32

Gnomad AFR AF: 0.654

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.956

Gnomad ASJ AF: 0.976

Gnomad EAS AF: 0.967

Gnomad SAS AF: 0.908

Gnomad FIN AF: 0.999

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.996

Gnomad OTH AF: 0.917

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

GnomAD4 genome AF: 0.893 AC: 135989 AN: 152200 Hom.: 62478 Cov.: 32 AF XY: 0.895 AC XY: 66611 AN XY: 74426

African (AFR) AF: 0.653 AC: 27092 AN: 41458

American (AMR) AF: 0.956 AC: 14620 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.976 AC: 3389 AN: 3472

East Asian (EAS) AF: 0.967 AC: 5015 AN: 5186

South Asian (SAS) AF: 0.908 AC: 4376 AN: 4822

European-Finnish (FIN) AF: 0.999 AC: 10601 AN: 10612

Middle Eastern (MID) AF: 0.939 AC: 276 AN: 294

European-Non Finnish (NFE) AF: 0.996 AC: 67771 AN: 68036

Other (OTH) AF: 0.918 AC: 1937 AN: 2110

Alfa AF: 0.962 Hom.: 193554

Bravo AF: 0.882

Asia WGS AF: 0.922 AC: 3202 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.6
DANN	Benign	0.78
PhyloP100		0.095

Splicing

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

Other links and lift over

dbSNP: rs2148065; hg19: chr13-95634313;