rs2024134

Variant names:

• chr17-11210815-T-G
• rs2024134
• ENST00000648331.1:n.99-11125A>C

Variant summary

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

The ENST00000648331.1(ENSG00000285541):​n.99-11125A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.682 in 151,518 control chromosomes in the GnomAD database, including 39,007 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 0.68 (39007 hom., cov: 29)
• Consequence: ENSG00000285541 ENST00000648331.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.529
• Publications: 5 publications found

Genes affected

ENSG00000285541 (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 (NFE) allele frequency at 95% confidence interval = 0.832 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
ENSG00000285541	ENST00000648331.1	n.99-11125A>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.682 AC: 103283 AN: 151400 Hom.: 39011 Cov.: 29

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.941

Gnomad AMR AF: 0.741

Gnomad ASJ AF: 0.783

Gnomad EAS AF: 0.647

Gnomad SAS AF: 0.687

Gnomad FIN AF: 0.907

Gnomad MID AF: 0.780

Gnomad NFE AF: 0.837

Gnomad OTH AF: 0.689

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

GnomAD4 genome AF: 0.682 AC: 103289 AN: 151518 Hom.: 39007 Cov.: 29 AF XY: 0.684 AC XY: 50618 AN XY: 73984

African (AFR) AF: 0.336 AC: 13847 AN: 41270

American (AMR) AF: 0.741 AC: 11278 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.783 AC: 2717 AN: 3468

East Asian (EAS) AF: 0.647 AC: 3316 AN: 5122

South Asian (SAS) AF: 0.686 AC: 3277 AN: 4776

European-Finnish (FIN) AF: 0.907 AC: 9482 AN: 10460

Middle Eastern (MID) AF: 0.767 AC: 224 AN: 292

European-Non Finnish (NFE) AF: 0.837 AC: 56851 AN: 67900

Other (OTH) AF: 0.686 AC: 1443 AN: 2102

Alfa AF: 0.785 Hom.: 179233

Bravo AF: 0.654

Asia WGS AF: 0.623 AC: 2167 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	0.56
DANN	Benign	0.77
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs2024134; hg19: chr17-11114132;