chr12-41810035-C-T

Variant names:

• chr12-41810035-C-T
• rs1817957

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 0.885 in 152,210 control chromosomes in the GnomAD database, including 59,739 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 0.88 (59739 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.921
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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: 0.885 AC: 134531 AN: 152092 Hom.: 59677 Cov.: 32

Gnomad AFR AF: 0.915

Gnomad AMI AF: 0.873

Gnomad AMR AF: 0.897

Gnomad ASJ AF: 0.877

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.919

Gnomad FIN AF: 0.875

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.854

Gnomad OTH AF: 0.881

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

GnomAD4 genome AF: 0.885 AC: 134651 AN: 152210 Hom.: 59739 Cov.: 32 AF XY: 0.888 AC XY: 66100 AN XY: 74412

African (AFR) AF: 0.915 AC: 38022 AN: 41534

American (AMR) AF: 0.898 AC: 13716 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.877 AC: 3044 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5176 AN: 5182

South Asian (SAS) AF: 0.920 AC: 4434 AN: 4822

European-Finnish (FIN) AF: 0.875 AC: 9280 AN: 10604

Middle Eastern (MID) AF: 0.901 AC: 265 AN: 294

European-Non Finnish (NFE) AF: 0.854 AC: 58052 AN: 67994

Other (OTH) AF: 0.882 AC: 1866 AN: 2116

Alfa AF: 0.865 Hom.: 94020

Bravo AF: 0.889

Asia WGS AF: 0.943 AC: 3281 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.29
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs1817957; hg19: chr12-42203837;