rs9566236

Variant names:

• chr13-37610028-A-G
• rs9566236
• ENST00000744989.1:n.48+12991A>G

Variant summary

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

The ENST00000744989.1(ENSG00000297050):​n.48+12991A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 152,078 control chromosomes in the GnomAD database, including 7,012 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 0.29 (7012 hom., cov: 32)
• Consequence: ENSG00000297050 ENST00000744989.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.628
• Publications: 1 publications found

Genes affected

ENSG00000297050 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.348 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
ENSG00000297050	ENST00000744989.1	n.48+12991A>G		intron_variant	Intron 1 of 4
ENSG00000297050	ENST00000744990.1	n.70+12991A>G		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.294 AC: 44721 AN: 151960 Hom.: 7002 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.294 AC: 44749 AN: 152078 Hom.: 7012 Cov.: 32 AF XY: 0.285 AC XY: 21216 AN XY: 74356

African (AFR) AF: 0.206 AC: 8542 AN: 41480

American (AMR) AF: 0.291 AC: 4445 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.493 AC: 1710 AN: 3468

East Asian (EAS) AF: 0.161 AC: 833 AN: 5166

South Asian (SAS) AF: 0.334 AC: 1611 AN: 4824

European-Finnish (FIN) AF: 0.254 AC: 2678 AN: 10564

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.352 AC: 23935 AN: 67984

Other (OTH) AF: 0.314 AC: 663 AN: 2114

Alfa AF: 0.333 Hom.: 1790

Bravo AF: 0.295

Asia WGS AF: 0.258 AC: 896 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.3
DANN	Benign	0.63
PhyloP100		0.63

Splicing

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

Other links and lift over

dbSNP: rs9566236; hg19: chr13-38184165; COSMIC: COSV69347291;