13-109605379-T-C

Position:

• chr13-109605379-T-C

Variant summary

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

The ENST00000650264.1(ENSG00000285534):​n.759-34221A>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 0.448 in 152,064 control chromosomes in the GnomAD database, including 15,817 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 0.45 (15817 hom., cov: 33)
• Consequence: ENST00000650264.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.18

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.563 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124903210	XR_007063870.1	n.940+830A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000650264.1	n.759-34221A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.448 AC: 68117 AN: 151946 Hom.: 15794 Cov.: 33

Gnomad AFR AF: 0.548

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.555

Gnomad SAS AF: 0.580

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.448 AC: 68186 AN: 152064 Hom.: 15817 Cov.: 33 AF XY: 0.452 AC XY: 33609 AN XY: 74334

Gnomad4 AFR AF: 0.548

Gnomad4 AMR AF: 0.465

Gnomad4 ASJ AF: 0.374

Gnomad4 EAS AF: 0.555

Gnomad4 SAS AF: 0.581

Gnomad4 FIN AF: 0.359

Gnomad4 NFE AF: 0.386

Gnomad4 OTH AF: 0.436

Alfa AF: 0.406 Hom.: 18221

Bravo AF: 0.456

Asia WGS AF: 0.532 AC: 1850 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.0
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6492208; hg19: chr13-110257726;