17-63901188-A-G

Variant names:

• chr17-63901188-A-G
• rs2941551
• ENST00000791140.1:n.500A>G

Variant summary

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

The ENST00000791140.1(ENSG00000303015):​n.500A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.287 in 145,798 control chromosomes in the GnomAD database, including 6,157 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 (6157 hom., cov: 33)
• Consequence: ENSG00000303015 ENST00000791140.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.119
• Publications: 14 publications found

Genes affected

ENSG00000303015 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.366 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000791140.1. 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
	ENSG00000303015	ENST00000791140.1		n.500A>G		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000303015	ENST00000791137.1		n.265+6016A>G		intron	N/A
	ENSG00000303015	ENST00000791138.1		n.462+308A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.287 AC: 41872 AN: 145690 Hom.: 6147 Cov.: 33

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.0612

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.376

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.287 AC: 41909 AN: 145798 Hom.: 6157 Cov.: 33 AF XY: 0.280 AC XY: 19961 AN XY: 71170

African (AFR) AF: 0.371 AC: 14385 AN: 38754

American (AMR) AF: 0.225 AC: 3268 AN: 14510

Ashkenazi Jewish (ASJ) AF: 0.272 AC: 927 AN: 3406

East Asian (EAS) AF: 0.0614 AC: 288 AN: 4694

South Asian (SAS) AF: 0.186 AC: 830 AN: 4452

European-Finnish (FIN) AF: 0.212 AC: 2162 AN: 10176

Middle Eastern (MID) AF: 0.381 AC: 109 AN: 286

European-Non Finnish (NFE) AF: 0.287 AC: 19118 AN: 66588

Other (OTH) AF: 0.275 AC: 560 AN: 2034

Alfa AF: 0.230 Hom.: 1094

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	5.3
DANN	Benign	0.39
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs2941551; hg19: chr17-61978548; COSMIC: COSV60242153;