rs900253

Variant names:

• chr12-40108943-T-C
• rs900253

Your query was ambiguous. Multiple possible variants found:

• chr12-40108943-T-C
• chr12-40108943-T-G

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 0.587 in 152,040 control chromosomes in the GnomAD database, including 26,515 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 0.59 (26515 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.522
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.67 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: 0.586 AC: 89097 AN: 151922 Hom.: 26479 Cov.: 32

Gnomad AFR AF: 0.653

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.680

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.681

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.565

Gnomad MID AF: 0.643

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.583

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

GnomAD4 genome AF: 0.587 AC: 89188 AN: 152040 Hom.: 26515 Cov.: 32 AF XY: 0.593 AC XY: 44048 AN XY: 74294

African (AFR) AF: 0.653 AC: 27063 AN: 41440

American (AMR) AF: 0.681 AC: 10401 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.576 AC: 2000 AN: 3470

East Asian (EAS) AF: 0.682 AC: 3533 AN: 5180

South Asian (SAS) AF: 0.553 AC: 2658 AN: 4810

European-Finnish (FIN) AF: 0.565 AC: 5962 AN: 10560

Middle Eastern (MID) AF: 0.627 AC: 183 AN: 292

European-Non Finnish (NFE) AF: 0.524 AC: 35634 AN: 67982

Other (OTH) AF: 0.581 AC: 1230 AN: 2116

Alfa AF: 0.547 Hom.: 12233

Bravo AF: 0.597

Asia WGS AF: 0.611 AC: 2127 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.3
DANN	Benign	0.64
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs900253; hg19: chr12-40502745;