5-13458257-G-A

Variant names:

• chr5-13458257-G-A
• rs1373992
• XR_001742606.2:n.503-62039C>T

Variant summary

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

The XR_001742606.2(LOC105374660):​n.503-62039C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 151,856 control chromosomes in the GnomAD database, including 3,033 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 0.19 (3033 hom., cov: 32)
• Consequence: LOC105374660 XR_001742606.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0610
• Publications: 5 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.345 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29119 AN: 151738 Hom.: 3028 Cov.: 32

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.192 AC: 29130 AN: 151856 Hom.: 3033 Cov.: 32 AF XY: 0.198 AC XY: 14662 AN XY: 74212

African (AFR) AF: 0.159 AC: 6566 AN: 41422

American (AMR) AF: 0.216 AC: 3292 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 494 AN: 3468

East Asian (EAS) AF: 0.358 AC: 1834 AN: 5120

South Asian (SAS) AF: 0.255 AC: 1229 AN: 4812

European-Finnish (FIN) AF: 0.229 AC: 2413 AN: 10534

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.185 AC: 12583 AN: 67916

Other (OTH) AF: 0.198 AC: 417 AN: 2106

Alfa AF: 0.190 Hom.: 7735

Bravo AF: 0.193

Asia WGS AF: 0.314 AC: 1092 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.1
DANN	Benign	0.52
PhyloP100		-0.061

Splicing

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

Other links and lift over

dbSNP: rs1373992; hg19: chr5-13458367; COSMIC: COSV66933287;