5-13496350-C-T

Variant summary

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

The XR_001742606.2(LOC105374660):n.502+80242G>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 0.624 in 151,676 control chromosomes in the GnomAD database, including 31,001 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 0.62 (31001 hom., cov: 32)
• Consequence: LOC105374660 XR_001742606.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.08

Genes affected

LOC105374660 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.832 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374660	XR_001742606.2	n.502+80242G>A		intron_variant, non_coding_transcript_variant
LOC105374660	XR_007058696.1	n.766+19985G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.624 AC: 94600 AN: 151556 Hom.: 30951 Cov.: 32

Gnomad AFR AF: 0.839

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.538

Gnomad EAS AF: 0.676

Gnomad SAS AF: 0.503

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.597

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

GnomAD4 genome AF: 0.624 AC: 94702 AN: 151676 Hom.: 31001 Cov.: 32 AF XY: 0.622 AC XY: 46062 AN XY: 74098

Gnomad4 AFR AF: 0.839

Gnomad4 AMR AF: 0.548

Gnomad4 ASJ AF: 0.538

Gnomad4 EAS AF: 0.677

Gnomad4 SAS AF: 0.501

Gnomad4 FIN AF: 0.575

Gnomad4 NFE AF: 0.531

Gnomad4 OTH AF: 0.593

Alfa AF: 0.596 Hom.: 3453

Bravo AF: 0.630

Asia WGS AF: 0.583 AC: 2016 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.91
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs230054; hg19: chr5-13496460;