rs13165478

Variant names:

• chr5-154489480-G-A
• rs13165478

Your query was ambiguous. Multiple possible variants found:

• chr5-154489480-G-A
• chr5-154489480-G-C
• chr5-154489480-G-T

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 0.4 in 151,756 control chromosomes in the GnomAD database, including 12,821 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 0.40 (12821 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.04
• Publications: 27 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.53 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.400 AC: 60675 AN: 151638 Hom.: 12812 Cov.: 31

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.453

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.400 AC: 60729 AN: 151756 Hom.: 12821 Cov.: 31 AF XY: 0.397 AC XY: 29408 AN XY: 74118

African (AFR) AF: 0.535 AC: 22138 AN: 41346

American (AMR) AF: 0.323 AC: 4935 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.289 AC: 1003 AN: 3468

East Asian (EAS) AF: 0.359 AC: 1851 AN: 5160

South Asian (SAS) AF: 0.219 AC: 1051 AN: 4806

European-Finnish (FIN) AF: 0.377 AC: 3953 AN: 10494

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.361 AC: 24506 AN: 67904

Other (OTH) AF: 0.378 AC: 799 AN: 2114

Alfa AF: 0.370 Hom.: 36623

Bravo AF: 0.407

Asia WGS AF: 0.282 AC: 978 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.3
DANN	Benign	0.61
PhyloP100		2.0

Splicing

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

Other links and lift over

dbSNP: rs13165478; hg19: chr5-153869040;