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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.586 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

Gnomad4 AFR AF: 0.653

Gnomad4 AMR AF: 0.681

Gnomad4 ASJ AF: 0.576

Gnomad4 EAS AF: 0.682

Gnomad4 SAS AF: 0.553

Gnomad4 FIN AF: 0.565

Gnomad4 NFE AF: 0.524

Gnomad4 OTH AF: 0.581

Alfa AF: 0.549 Hom.: 11130

Bravo AF: 0.597

Asia WGS AF: 0.611 AC: 2127 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs900253; hg19: chr12-40502745;