15-94727238-C-T

Variant names:

• chr15-94727238-C-T
• rs7173947
• ENST00000801101.1:n.182+961G>A

Variant summary

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

The ENST00000801101.1(ENSG00000286917):​n.182+961G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.614 in 151,944 control chromosomes in the GnomAD database, including 28,946 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 0.61 (28946 hom., cov: 32)
• Consequence: ENSG00000286917 ENST00000801101.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.02
• Publications: 16 publications found

Genes affected

ENSG00000286917 (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 (SAS) allele frequency at 95% confidence interval = 0.726 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000801101.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286917	ENST00000801101.1		n.182+961G>A		intron	N/A
	ENSG00000286917	ENST00000801102.1		n.158+961G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.614 AC: 93201 AN: 151826 Hom.: 28929 Cov.: 32

Gnomad AFR AF: 0.542

Gnomad AMI AF: 0.614

Gnomad AMR AF: 0.669

Gnomad ASJ AF: 0.741

Gnomad EAS AF: 0.682

Gnomad SAS AF: 0.745

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.635

Gnomad OTH AF: 0.631

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

GnomAD4 genome AF: 0.614 AC: 93265 AN: 151944 Hom.: 28946 Cov.: 32 AF XY: 0.615 AC XY: 45679 AN XY: 74234

African (AFR) AF: 0.542 AC: 22442 AN: 41436

American (AMR) AF: 0.669 AC: 10213 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.741 AC: 2567 AN: 3464

East Asian (EAS) AF: 0.683 AC: 3518 AN: 5152

South Asian (SAS) AF: 0.747 AC: 3596 AN: 4816

European-Finnish (FIN) AF: 0.539 AC: 5689 AN: 10552

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.635 AC: 43153 AN: 67938

Other (OTH) AF: 0.626 AC: 1324 AN: 2114

Alfa AF: 0.635 Hom.: 141650

Bravo AF: 0.622

Asia WGS AF: 0.689 AC: 2395 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	14
DANN	Benign	0.45
PhyloP100		2.0

Splicing

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

Other links and lift over

dbSNP: rs7173947; hg19: chr15-95270467;