rs9550642

Variant names:

• chr13-20375953-G-A
• rs9550642
• ENST00000737415.1:n.262-9523C>T

Variant summary

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

The ENST00000737415.1(ENSG00000296216):​n.262-9523C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0909 in 152,168 control chromosomes in the GnomAD database, including 920 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 0.091 (920 hom., cov: 32)
• Consequence: ENSG00000296216 ENST00000737415.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 6 publications found

Genes affected

ENSG00000296216 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.277 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
ENSG00000296216	ENST00000737415.1	n.262-9523C>T		intron_variant	Intron 1 of 1
ENSG00000296216	ENST00000737416.1	n.181-9523C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0909 AC: 13827 AN: 152050 Hom.: 919 Cov.: 32

Gnomad AFR AF: 0.0233

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.0895

Gnomad MID AF: 0.0669

Gnomad NFE AF: 0.0975

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.0909 AC: 13829 AN: 152168 Hom.: 920 Cov.: 32 AF XY: 0.0932 AC XY: 6936 AN XY: 74398

African (AFR) AF: 0.0233 AC: 967 AN: 41540

American (AMR) AF: 0.129 AC: 1973 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 452 AN: 3472

East Asian (EAS) AF: 0.289 AC: 1490 AN: 5156

South Asian (SAS) AF: 0.225 AC: 1081 AN: 4810

European-Finnish (FIN) AF: 0.0895 AC: 948 AN: 10594

Middle Eastern (MID) AF: 0.0582 AC: 17 AN: 292

European-Non Finnish (NFE) AF: 0.0975 AC: 6632 AN: 67994

Other (OTH) AF: 0.105 AC: 221 AN: 2108

Alfa AF: 0.0949 Hom.: 990

Bravo AF: 0.0921

Asia WGS AF: 0.218 AC: 758 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.53
DANN	Benign	0.26
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs9550642; hg19: chr13-20950092;