rs17527491

Variant names:

• chr10-22738652-G-A
• rs17527491
• ENST00000756996.1:n.497-5607C>T

Variant summary

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

The ENST00000756996.1(ENSG00000298626):​n.497-5607C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 151,998 control chromosomes in the GnomAD database, including 2,918 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 0.18 (2918 hom., cov: 31)
• Consequence: ENSG00000298626 ENST00000756996.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.566
• Publications: 2 publications found

Genes affected

ENSG00000298626 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.265 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
ENSG00000298626	ENST00000756996.1	n.497-5607C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26666 AN: 151880 Hom.: 2917 Cov.: 31

Gnomad AFR AF: 0.0519

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.0819

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.175 AC: 26666 AN: 151998 Hom.: 2918 Cov.: 31 AF XY: 0.172 AC XY: 12815 AN XY: 74294

African (AFR) AF: 0.0517 AC: 2146 AN: 41490

American (AMR) AF: 0.160 AC: 2449 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 587 AN: 3466

East Asian (EAS) AF: 0.0821 AC: 425 AN: 5178

South Asian (SAS) AF: 0.277 AC: 1329 AN: 4796

European-Finnish (FIN) AF: 0.183 AC: 1930 AN: 10546

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.252 AC: 17113 AN: 67928

Other (OTH) AF: 0.197 AC: 416 AN: 2108

Alfa AF: 0.225 Hom.: 13326

Bravo AF: 0.165

Asia WGS AF: 0.165 AC: 575 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.38
DANN	Benign	0.63
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs17527491; hg19: chr10-23027581;