chr13-109484797-G-T

Position:

• chr13-109484797-G-T

Variant summary

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

The ENST00000650264.1(ENSG00000285534):​n.934-5477C>A 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 0.147 in 152,002 control chromosomes in the GnomAD database, including 2,256 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 0.15 (2256 hom., cov: 33)
• Consequence: ENST00000650264.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.277 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.934-5477C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22299 AN: 151884 Hom.: 2260 Cov.: 33

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.0795

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.0724

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.0661

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.0951

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.147 AC: 22288 AN: 152002 Hom.: 2256 Cov.: 33 AF XY: 0.146 AC XY: 10814 AN XY: 74300

Gnomad4 AFR AF: 0.282

Gnomad4 AMR AF: 0.0792

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.0724

Gnomad4 SAS AF: 0.204

Gnomad4 FIN AF: 0.0661

Gnomad4 NFE AF: 0.0951

Gnomad4 OTH AF: 0.126

Alfa AF: 0.0976 Hom.: 1068

Bravo AF: 0.150

Asia WGS AF: 0.109 AC: 378 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.086
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11620131; hg19: chr13-110137144;