rs1547241

Positions:

• 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, non coding transcript 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: ENST00000650264.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000650264.1	n.759-50100G>C		intron_variant, non_coding_transcript_variant

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;