5-13496350-C-T

Variant names:

• chr5-13496350-C-T
• rs230054
• XR_001742606.2:n.502+80242G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001742606.2(LOC105374660):​n.502+80242G>A variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.08
• Publications: 2 publications found

Genes affected

LOC105374660 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC105374660	XR_001742606.2	n.502+80242G>A		intron_variant	Intron 3 of 3
LOC105374660	XR_007058696.1	n.766+19985G>A		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.839 AC: 34825 AN: 41486

American (AMR) AF: 0.548 AC: 8354 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.538 AC: 1864 AN: 3462

East Asian (EAS) AF: 0.677 AC: 3497 AN: 5168

South Asian (SAS) AF: 0.501 AC: 2408 AN: 4802

European-Finnish (FIN) AF: 0.575 AC: 5995 AN: 10420

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.531 AC: 35984 AN: 67790

Other (OTH) AF: 0.593 AC: 1247 AN: 2104

Alfa AF: 0.606 Hom.: 3722

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
PhyloP100		-3.1

Splicing

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

Other links and lift over

dbSNP: rs230054; hg19: chr5-13496460;