rs13174348

Positions:

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

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

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

Gnomad4 AFR AF: 0.610

Gnomad4 AMR AF: 0.437

Gnomad4 ASJ AF: 0.292

Gnomad4 EAS AF: 0.327

Gnomad4 SAS AF: 0.320

Gnomad4 FIN AF: 0.167

Gnomad4 NFE AF: 0.223

Gnomad4 OTH AF: 0.349

Alfa AF: 0.265 Hom.: 5943

Bravo AF: 0.389

Asia WGS AF: 0.333 AC: 1158 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13174348; hg19: chr5-115138748;