1-188414185-T-C

Variant names:

• chr1-188414185-T-C
• rs12142669

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 0.813 in 151,660 control chromosomes in the GnomAD database, including 50,292 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 0.81 (50292 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.218
• Publications: 3 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 (AMR) allele frequency at 95% confidence interval = 0.831 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: 0.813 AC: 123195 AN: 151542 Hom.: 50256 Cov.: 31

Gnomad AFR AF: 0.749

Gnomad AMI AF: 0.942

Gnomad AMR AF: 0.840

Gnomad ASJ AF: 0.788

Gnomad EAS AF: 0.755

Gnomad SAS AF: 0.839

Gnomad FIN AF: 0.890

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.836

Gnomad OTH AF: 0.794

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

GnomAD4 genome AF: 0.813 AC: 123285 AN: 151660 Hom.: 50292 Cov.: 31 AF XY: 0.817 AC XY: 60525 AN XY: 74126

African (AFR) AF: 0.749 AC: 31039 AN: 41430

American (AMR) AF: 0.840 AC: 12749 AN: 15170

Ashkenazi Jewish (ASJ) AF: 0.788 AC: 2724 AN: 3458

East Asian (EAS) AF: 0.754 AC: 3881 AN: 5146

South Asian (SAS) AF: 0.840 AC: 4050 AN: 4822

European-Finnish (FIN) AF: 0.890 AC: 9423 AN: 10588

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.836 AC: 56648 AN: 67734

Other (OTH) AF: 0.795 AC: 1674 AN: 2106

Alfa AF: 0.824 Hom.: 76352

Bravo AF: 0.807

Asia WGS AF: 0.816 AC: 2839 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	0.71
DANN	Benign	0.48
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs12142669; hg19: chr1-188383316;