rs12500918

Variant names:

• chr4-152747856-A-C
• rs12500918

Your query was ambiguous. Multiple possible variants found:

• chr4-152747856-A-C
• chr4-152747856-A-G
• chr4-152747856-A-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 0.482 in 152,036 control chromosomes in the GnomAD database, including 17,847 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 0.48 (17847 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.09
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.572 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: 0.482 AC: 73203 AN: 151918 Hom.: 17816 Cov.: 33

Gnomad AFR AF: 0.511

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.591

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.482 AC: 73276 AN: 152036 Hom.: 17847 Cov.: 33 AF XY: 0.488 AC XY: 36257 AN XY: 74326

African (AFR) AF: 0.511 AC: 21202 AN: 41460

American (AMR) AF: 0.468 AC: 7149 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.371 AC: 1286 AN: 3470

East Asian (EAS) AF: 0.533 AC: 2760 AN: 5182

South Asian (SAS) AF: 0.590 AC: 2848 AN: 4824

European-Finnish (FIN) AF: 0.534 AC: 5632 AN: 10538

Middle Eastern (MID) AF: 0.425 AC: 124 AN: 292

European-Non Finnish (NFE) AF: 0.453 AC: 30823 AN: 67978

Other (OTH) AF: 0.452 AC: 954 AN: 2110

Alfa AF: 0.452 Hom.: 53247

Bravo AF: 0.473

Asia WGS AF: 0.551 AC: 1913 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	15
DANN	Benign	0.48
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs12500918; hg19: chr4-153669008;