chr13-54949643-A-G

Position:

• chr13-54949643-A-G

Variant summary

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

The XM_047430847.1(LOC124903233):​c.161-2658A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.703 in 152,090 control chromosomes in the GnomAD database, including 38,814 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 0.70 (38814 hom., cov: 33)
• Consequence: LOC124903233 XM_047430847.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.451

Genes affected

LOC124903233 (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 (NFE) allele frequency at 95% confidence interval = 0.796 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124903233	XM_047430847.1	c.161-2658A>G		intron_variant			XP_047286803.1
LOC124903233	XM_047430848.1	c.161-2658A>G		intron_variant			XP_047286804.1
LOC124903233	XR_007063910.1	n.281-2658A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000277047	ENST00000616396.2	n.166-2658A>G		intron_variant		3
ENSG00000277047	ENST00000622486.5	n.169-2658A>G		intron_variant		3
ENSG00000277047	ENST00000653085.1	n.172-2658A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.703 AC: 106882 AN: 151972 Hom.: 38806 Cov.: 33

Gnomad AFR AF: 0.512

Gnomad AMI AF: 0.675

Gnomad AMR AF: 0.753

Gnomad ASJ AF: 0.817

Gnomad EAS AF: 0.642

Gnomad SAS AF: 0.695

Gnomad FIN AF: 0.738

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.802

Gnomad OTH AF: 0.728

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

GnomAD4 genome AF: 0.703 AC: 106923 AN: 152090 Hom.: 38814 Cov.: 33 AF XY: 0.701 AC XY: 52109 AN XY: 74352

Gnomad4 AFR AF: 0.512

Gnomad4 AMR AF: 0.753

Gnomad4 ASJ AF: 0.817

Gnomad4 EAS AF: 0.642

Gnomad4 SAS AF: 0.696

Gnomad4 FIN AF: 0.738

Gnomad4 NFE AF: 0.802

Gnomad4 OTH AF: 0.720

Alfa AF: 0.770 Hom.: 20463

Bravo AF: 0.695

Asia WGS AF: 0.612 AC: 2129 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	7.1
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9536919; hg19: chr13-55523778;