rs1547241

Variant names:

• chr13-109621258-C-G
• rs1547241
• ENST00000650264.1:n.759-50100G>C

Your query was ambiguous. Multiple possible variants found:

• chr13-109621258-C-G
• chr13-109621258-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000650264.1(ENSG00000285534):​n.759-50100G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.677 in 151,992 control chromosomes in the GnomAD database, including 35,482 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 (35482 hom., cov: 32)
• Consequence: ENSG00000285534 ENST00000650264.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53

Genes affected

ENSG00000285534 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.899 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
ENSG00000285534	ENST00000650264.1	n.759-50100G>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.677 AC: 102755 AN: 151874 Hom.: 35421 Cov.: 32

Gnomad AFR AF: 0.777

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.653

Gnomad ASJ AF: 0.697

Gnomad EAS AF: 0.920

Gnomad SAS AF: 0.846

Gnomad FIN AF: 0.589

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.680

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

GnomAD4 genome AF: 0.677 AC: 102872 AN: 151992 Hom.: 35482 Cov.: 32 AF XY: 0.682 AC XY: 50663 AN XY: 74282

Gnomad4 AFR AF: 0.778

Gnomad4 AMR AF: 0.653

Gnomad4 ASJ AF: 0.697

Gnomad4 EAS AF: 0.921

Gnomad4 SAS AF: 0.847

Gnomad4 FIN AF: 0.589

Gnomad4 NFE AF: 0.605

Gnomad4 OTH AF: 0.679

Alfa AF: 0.646 Hom.: 3756

Bravo AF: 0.678

Asia WGS AF: 0.846 AC: 2942 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.37
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1547241; hg19: chr13-110273605;