rs1152004

Variant names:

• chr3-12441605-A-G
• rs1152004

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 0.194 in 151,998 control chromosomes in the GnomAD database, including 3,042 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 0.19 (3042 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.591
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.206 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: 0.194 AC: 29412 AN: 151880 Hom.: 3038 Cov.: 31

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.0451

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.0748

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.194 AC: 29433 AN: 151998 Hom.: 3042 Cov.: 31 AF XY: 0.193 AC XY: 14307 AN XY: 74310

African (AFR) AF: 0.186 AC: 7721 AN: 41436

American (AMR) AF: 0.204 AC: 3124 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.226 AC: 785 AN: 3472

East Asian (EAS) AF: 0.0749 AC: 385 AN: 5138

South Asian (SAS) AF: 0.134 AC: 646 AN: 4810

European-Finnish (FIN) AF: 0.187 AC: 1977 AN: 10578

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.209 AC: 14195 AN: 67962

Other (OTH) AF: 0.236 AC: 498 AN: 2112

Alfa AF: 0.203 Hom.: 9671

Bravo AF: 0.192

Asia WGS AF: 0.193 AC: 675 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	6.0
DANN	Benign	0.39
PhyloP100		0.59

Splicing

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

Other links and lift over

dbSNP: rs1152004; hg19: chr3-12483104;