rs8001186

Variant names:

• chr13-109724508-T-G
• rs8001186
• ENST00000650264.1:n.758+6435A>C

Variant summary

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

The ENST00000650264.1(ENSG00000285534):​n.758+6435A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 151,956 control chromosomes in the GnomAD database, including 9,476 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 0.35 (9476 hom., cov: 32)
• Consequence: ENSG00000285534 ENST00000650264.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0610
• Publications: 7 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.385 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.758+6435A>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52716 AN: 151838 Hom.: 9462 Cov.: 32

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.347 AC: 52767 AN: 151956 Hom.: 9476 Cov.: 32 AF XY: 0.350 AC XY: 26014 AN XY: 74250

African (AFR) AF: 0.390 AC: 16156 AN: 41420

American (AMR) AF: 0.352 AC: 5372 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.393 AC: 1365 AN: 3470

East Asian (EAS) AF: 0.154 AC: 794 AN: 5158

South Asian (SAS) AF: 0.283 AC: 1365 AN: 4816

European-Finnish (FIN) AF: 0.444 AC: 4677 AN: 10542

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.324 AC: 22010 AN: 67968

Other (OTH) AF: 0.349 AC: 734 AN: 2106

Alfa AF: 0.196 Hom.: 476

Bravo AF: 0.343

Asia WGS AF: 0.257 AC: 897 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.9
DANN	Benign	0.69
PhyloP100		-0.061

Splicing

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

Other links and lift over

dbSNP: rs8001186; hg19: chr13-110376855;