rs1152007

Variant names:

• chr3-12446048-G-C
• rs1152007

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.704 in 152,150 control chromosomes in the GnomAD database, including 38,509 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 0.70 (38509 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.821 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: 0.704 AC: 107075 AN: 152032 Hom.: 38461 Cov.: 33

Gnomad AFR AF: 0.827

Gnomad AMI AF: 0.817

Gnomad AMR AF: 0.696

Gnomad ASJ AF: 0.625

Gnomad EAS AF: 0.523

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.729

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.692

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

GnomAD4 genome AF: 0.704 AC: 107179 AN: 152150 Hom.: 38509 Cov.: 33 AF XY: 0.702 AC XY: 52188 AN XY: 74372

Gnomad4 AFR AF: 0.828

Gnomad4 AMR AF: 0.695

Gnomad4 ASJ AF: 0.625

Gnomad4 EAS AF: 0.523

Gnomad4 SAS AF: 0.483

Gnomad4 FIN AF: 0.729

Gnomad4 NFE AF: 0.660

Gnomad4 OTH AF: 0.689

Alfa AF: 0.702 Hom.: 4698

Bravo AF: 0.714

Asia WGS AF: 0.559 AC: 1944 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.47
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1152007; hg19: chr3-12487547;