rs12500612

Variant names:

• chr4-24739335-G-T
• rs12500612

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 0.106 in 152,138 control chromosomes in the GnomAD database, including 959 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 0.11 (959 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.715
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.13 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: 0.106 AC: 16169 AN: 152022 Hom.: 962 Cov.: 32

Gnomad AFR AF: 0.0824

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0976

Gnomad FIN AF: 0.0546

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.106 AC: 16166 AN: 152138 Hom.: 959 Cov.: 32 AF XY: 0.102 AC XY: 7608 AN XY: 74358

African (AFR) AF: 0.0824 AC: 3418 AN: 41502

American (AMR) AF: 0.111 AC: 1695 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 551 AN: 3470

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5182

South Asian (SAS) AF: 0.0973 AC: 469 AN: 4820

European-Finnish (FIN) AF: 0.0546 AC: 578 AN: 10582

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.132 AC: 8992 AN: 67980

Other (OTH) AF: 0.145 AC: 307 AN: 2112

Alfa AF: 0.128 Hom.: 2540

Bravo AF: 0.109

Asia WGS AF: 0.0630 AC: 219 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.0
DANN	Benign	0.79
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs12500612; hg19: chr4-24740958;