rs12153048

Variant names:

• chr5-117177909-C-G
• rs12153048

Your query was ambiguous. Multiple possible variants found:

• chr5-117177909-C-G
• chr5-117177909-C-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 0.0752 in 152,120 control chromosomes in the GnomAD database, including 650 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 0.075 (650 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0590
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.155 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: 0.0752 AC: 11428 AN: 152002 Hom.: 650 Cov.: 32

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.0391

Gnomad ASJ AF: 0.0406

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0441

Gnomad FIN AF: 0.0500

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0477

Gnomad OTH AF: 0.0609

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

GnomAD4 genome AF: 0.0752 AC: 11442 AN: 152120 Hom.: 650 Cov.: 32 AF XY: 0.0720 AC XY: 5356 AN XY: 74340

African (AFR) AF: 0.158 AC: 6551 AN: 41494

American (AMR) AF: 0.0391 AC: 597 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0406 AC: 141 AN: 3470

East Asian (EAS) AF: 0.000194 AC: 1 AN: 5156

South Asian (SAS) AF: 0.0451 AC: 217 AN: 4808

European-Finnish (FIN) AF: 0.0500 AC: 529 AN: 10588

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0477 AC: 3243 AN: 68016

Other (OTH) AF: 0.0603 AC: 127 AN: 2106

Alfa AF: 0.0269 Hom.: 16

Bravo AF: 0.0777

Asia WGS AF: 0.0230 AC: 83 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	8.1
DANN	Benign	0.71
PhyloP100		0.059

Splicing

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

Other links and lift over

dbSNP: rs12153048; hg19: chr5-116513605; COSMIC: COSV60185923;