rs9536666

Variant names:

• chr13-54273057-G-A
• rs9536666
• ENST00000721339.1:n.284+3650G>A

Your query was ambiguous. Multiple possible variants found:

• chr13-54273057-G-A
• chr13-54273057-G-C
• chr13-54273057-G-T

Variant summary

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

The ENST00000721339.1(ENSG00000294129):​n.284+3650G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 151,368 control chromosomes in the GnomAD database, including 8,039 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 0.31 (8039 hom., cov: 31)
• Consequence: ENSG00000294129 ENST00000721339.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0430
• Publications: 4 publications found

Genes affected

ENSG00000294129 (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 = 0.723 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
ENSG00000294129	ENST00000721339.1	n.284+3650G>A		intron_variant	Intron 1 of 2
ENSG00000294129	ENST00000721340.1	n.349+3650G>A		intron_variant	Intron 1 of 2
ENSG00000294129	ENST00000721341.1	n.129+3650G>A		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46261 AN: 151252 Hom.: 8021 Cov.: 31

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.187

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.743

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.306 AC: 46324 AN: 151368 Hom.: 8039 Cov.: 31 AF XY: 0.309 AC XY: 22857 AN XY: 73930

African (AFR) AF: 0.383 AC: 15810 AN: 41302

American (AMR) AF: 0.298 AC: 4522 AN: 15192

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 797 AN: 3462

East Asian (EAS) AF: 0.743 AC: 3825 AN: 5148

South Asian (SAS) AF: 0.331 AC: 1592 AN: 4806

European-Finnish (FIN) AF: 0.207 AC: 2161 AN: 10418

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.247 AC: 16703 AN: 67726

Other (OTH) AF: 0.311 AC: 657 AN: 2110

Alfa AF: 0.266 Hom.: 18513

Bravo AF: 0.315

Asia WGS AF: 0.536 AC: 1863 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.5
DANN	Benign	0.81
PhyloP100		0.043

Splicing

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

Other links and lift over

dbSNP: rs9536666; hg19: chr13-54847192;