rs1632252

Variant names:

• chr12-43096740-G-C
• rs1632252

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 0.351 in 151,752 control chromosomes in the GnomAD database, including 9,675 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 0.35 (9675 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.384
• Publications: 1 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 (SAS) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.351 AC: 53266 AN: 151632 Hom.: 9662 Cov.: 32

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.0840

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.339

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

GnomAD4 genome AF: 0.351 AC: 53309 AN: 151752 Hom.: 9675 Cov.: 32 AF XY: 0.348 AC XY: 25809 AN XY: 74136

African (AFR) AF: 0.316 AC: 13081 AN: 41424

American (AMR) AF: 0.312 AC: 4750 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1190 AN: 3462

East Asian (EAS) AF: 0.0840 AC: 431 AN: 5128

South Asian (SAS) AF: 0.424 AC: 2044 AN: 4820

European-Finnish (FIN) AF: 0.372 AC: 3923 AN: 10536

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.392 AC: 26595 AN: 67844

Other (OTH) AF: 0.336 AC: 709 AN: 2108

Alfa AF: 0.383 Hom.: 1394

Bravo AF: 0.341

Asia WGS AF: 0.248 AC: 866 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.8
DANN	Benign	0.74
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs1632252; hg19: chr12-43490543;