13-109633131-T-C

Variant summary

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

The ENST00000650264.1(ENSG00000285534):n.759-61973A>G 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 0.493 in 151,760 control chromosomes in the GnomAD database, including 18,685 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 0.49 (18685 hom., cov: 30)
• Consequence: ENST00000650264.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.268

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.618 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000650264.1	n.759-61973A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.492 AC: 74679 AN: 151642 Hom.: 18662 Cov.: 30

Gnomad AFR AF: 0.522

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.636

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.493 AC: 74747 AN: 151760 Hom.: 18685 Cov.: 30 AF XY: 0.501 AC XY: 37136 AN XY: 74142

Gnomad4 AFR AF: 0.522

Gnomad4 AMR AF: 0.597

Gnomad4 ASJ AF: 0.439

Gnomad4 EAS AF: 0.636

Gnomad4 SAS AF: 0.615

Gnomad4 FIN AF: 0.455

Gnomad4 NFE AF: 0.442

Gnomad4 OTH AF: 0.487

Alfa AF: 0.462 Hom.: 22828

Bravo AF: 0.502

Asia WGS AF: 0.572 AC: 1990 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	5.5
Dann	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1929210; hg19: chr13-110285478;