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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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 v4.9

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;