rs17637161

Variant names:

• chr8-137859170-A-G
• rs17637161
• ENST00000518973.1:n.515-21285T>C

Your query was ambiguous. Multiple possible variants found:

• chr8-137859170-A-G
• chr8-137859170-A-T

Variant summary

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

The ENST00000518973.1(ENSG00000253288):​n.515-21285T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 152,062 control chromosomes in the GnomAD database, including 2,560 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 0.17 (2560 hom., cov: 32)
• Consequence: ENSG00000253288 ENST00000518973.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.888
• Publications: 1 publications found

Genes affected

ENSG00000253288 (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 = 0.221 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC401478	NR_161374.1	n.574-21285T>C		intron_variant	Intron 2 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253288	ENST00000518973.1	n.515-21285T>C		intron_variant	Intron 1 of 2	2
ENSG00000254361	ENST00000519652.3	n.314+2051A>G		intron_variant	Intron 2 of 2	4
ENSG00000253288	ENST00000657186.1	n.602-21285T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26314 AN: 151946 Hom.: 2552 Cov.: 32

Gnomad AFR AF: 0.0959

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.0555

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.173 AC: 26344 AN: 152062 Hom.: 2560 Cov.: 32 AF XY: 0.170 AC XY: 12650 AN XY: 74322

African (AFR) AF: 0.0963 AC: 3999 AN: 41512

American (AMR) AF: 0.173 AC: 2645 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.226 AC: 783 AN: 3468

East Asian (EAS) AF: 0.0556 AC: 287 AN: 5162

South Asian (SAS) AF: 0.123 AC: 593 AN: 4820

European-Finnish (FIN) AF: 0.196 AC: 2066 AN: 10552

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.224 AC: 15256 AN: 67972

Other (OTH) AF: 0.201 AC: 423 AN: 2106

Alfa AF: 0.199 Hom.: 551

Bravo AF: 0.167

Asia WGS AF: 0.0870 AC: 304 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	3.7
DANN	Benign	0.87
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs17637161; hg19: chr8-138871413;