rs2548145

Variant names:

• chr5-40134675-G-A
• rs2548145

Your query was ambiguous. Multiple possible variants found:

• chr5-40134675-G-A
• chr5-40134675-G-C
• chr5-40134675-G-T

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 0.552 in 151,696 control chromosomes in the GnomAD database, including 24,141 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 0.55 (24141 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.216

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 (EAS) allele frequency at 95% confidence interval = 0.783 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: 0.552 AC: 83710 AN: 151576 Hom.: 24093 Cov.: 29

Gnomad AFR AF: 0.676

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.617

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.804

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.530

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

GnomAD4 genome AF: 0.552 AC: 83812 AN: 151696 Hom.: 24141 Cov.: 29 AF XY: 0.553 AC XY: 40977 AN XY: 74108

Gnomad4 AFR AF: 0.676

Gnomad4 AMR AF: 0.618

Gnomad4 ASJ AF: 0.436

Gnomad4 EAS AF: 0.803

Gnomad4 SAS AF: 0.496

Gnomad4 FIN AF: 0.464

Gnomad4 NFE AF: 0.468

Gnomad4 OTH AF: 0.534

Alfa AF: 0.494 Hom.: 30126

Bravo AF: 0.576

Asia WGS AF: 0.626 AC: 2180 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	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2548145; hg19: chr5-40134777;