rs12510308

Variant names:

• chr4-128228725-G-T
• rs12510308

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 0.638 in 152,092 control chromosomes in the GnomAD database, including 33,162 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 0.64 (33162 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.206
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.746 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: 0.638 AC: 97027 AN: 151974 Hom.: 33151 Cov.: 33

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.779

Gnomad AMR AF: 0.742

Gnomad ASJ AF: 0.785

Gnomad EAS AF: 0.448

Gnomad SAS AF: 0.765

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.751

Gnomad OTH AF: 0.688

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

GnomAD4 genome AF: 0.638 AC: 97083 AN: 152092 Hom.: 33162 Cov.: 33 AF XY: 0.638 AC XY: 47443 AN XY: 74338

African (AFR) AF: 0.400 AC: 16567 AN: 41444

American (AMR) AF: 0.742 AC: 11321 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.785 AC: 2721 AN: 3468

East Asian (EAS) AF: 0.449 AC: 2321 AN: 5172

South Asian (SAS) AF: 0.765 AC: 3692 AN: 4826

European-Finnish (FIN) AF: 0.658 AC: 6962 AN: 10588

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.751 AC: 51088 AN: 68010

Other (OTH) AF: 0.692 AC: 1463 AN: 2114

Alfa AF: 0.715 Hom.: 152428

Bravo AF: 0.629

Asia WGS AF: 0.607 AC: 2110 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	4.1
DANN	Benign	0.71
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs12510308; hg19: chr4-129149880;