rs13024541

Variant names:

• chr2-62328602-T-C
• rs13024541
• ENST00000687402.3:n.199+32156T>C

Your query was ambiguous. Multiple possible variants found:

• chr2-62328602-T-C
• chr2-62328602-T-G

Variant summary

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

The ENST00000687402.3(ENSG00000228541):​n.199+32156T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.581 in 152,024 control chromosomes in the GnomAD database, including 25,847 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 0.58 (25847 hom., cov: 32)
• Consequence: ENSG00000228541 ENST00000687402.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47
• Publications: 9 publications found

Genes affected

ENSG00000228541 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.608 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
ENSG00000228541	ENST00000687402.3	n.199+32156T>C		intron_variant	Intron 1 of 1
ENSG00000228541	ENST00000687773.2	n.199+32156T>C		intron_variant	Intron 1 of 1
ENSG00000228541	ENST00000688476.3	n.202-17312T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.581 AC: 88216 AN: 151906 Hom.: 25816 Cov.: 32

Gnomad AFR AF: 0.514

Gnomad AMI AF: 0.609

Gnomad AMR AF: 0.601

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.557

Gnomad FIN AF: 0.638

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.613

Gnomad OTH AF: 0.568

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

GnomAD4 genome AF: 0.581 AC: 88316 AN: 152024 Hom.: 25847 Cov.: 32 AF XY: 0.582 AC XY: 43275 AN XY: 74318

African (AFR) AF: 0.514 AC: 21333 AN: 41472

American (AMR) AF: 0.601 AC: 9177 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.561 AC: 1946 AN: 3468

East Asian (EAS) AF: 0.557 AC: 2879 AN: 5170

South Asian (SAS) AF: 0.558 AC: 2692 AN: 4822

European-Finnish (FIN) AF: 0.638 AC: 6740 AN: 10562

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.613 AC: 41645 AN: 67946

Other (OTH) AF: 0.572 AC: 1206 AN: 2110

Alfa AF: 0.489 Hom.: 1383

Bravo AF: 0.576

Asia WGS AF: 0.581 AC: 2020 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.76
DANN	Benign	0.53
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs13024541; hg19: chr2-62555737;