rs13174348

Variant names:

• chr5-115803051-G-A
• rs13174348

Your query was ambiguous. Multiple possible variants found:

• chr5-115803051-G-A
• chr5-115803051-G-C

Variant summary

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

The variant allele was found at a frequency of 0.356 in 152,126 control chromosomes in the GnomAD database, including 11,991 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 0.36 (11991 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.321
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.604 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: 0.355 AC: 53973 AN: 152006 Hom.: 11943 Cov.: 32

Gnomad AFR AF: 0.609

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.292

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.312

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.356 AC: 54086 AN: 152126 Hom.: 11991 Cov.: 32 AF XY: 0.355 AC XY: 26383 AN XY: 74404

African (AFR) AF: 0.610 AC: 25297 AN: 41462

American (AMR) AF: 0.437 AC: 6684 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.292 AC: 1014 AN: 3468

East Asian (EAS) AF: 0.327 AC: 1697 AN: 5184

South Asian (SAS) AF: 0.320 AC: 1542 AN: 4818

European-Finnish (FIN) AF: 0.167 AC: 1773 AN: 10590

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.223 AC: 15156 AN: 67998

Other (OTH) AF: 0.349 AC: 737 AN: 2110

Alfa AF: 0.284 Hom.: 10483

Bravo AF: 0.389

Asia WGS AF: 0.333 AC: 1158 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.68
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs13174348; hg19: chr5-115138748;