rs2941551

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr17-63901188-A-C
• chr17-63901188-A-G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000791140.1(ENSG00000303015):​n.500A>C 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 0.0000271 in 147,476 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000027 (0 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: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

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
ENSG00000303015	ENST00000791140.1	n.500A>C		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000303015	ENST00000791137.1	n.265+6016A>C		intron_variant	Intron 1 of 1
ENSG00000303015	ENST00000791138.1	n.462+308A>C		intron_variant	Intron 2 of 2
ENSG00000303015	ENST00000791139.1	n.435+308A>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0000271 AC: 4 AN: 147364 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000681

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000623

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.0000271 AC: 4 AN: 147476 Hom.: 0 Cov.: 33 AF XY: 0.0000139 AC XY: 1 AN XY: 71966

African (AFR) AF: 0.00 AC: 0 AN: 39640

American (AMR) AF: 0.0000680 AC: 1 AN: 14702

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3416

East Asian (EAS) AF: 0.000625 AC: 3 AN: 4802

South Asian (SAS) AF: 0.00 AC: 0 AN: 4554

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10252

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 288

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 66864

Other (OTH) AF: 0.00 AC: 0 AN: 2056

Alfa AF: 0.00 Hom.: 1094

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.1
DANN	Benign	0.53
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;