1-18838033-C-T

Variant names:

• chr1-18838033-C-T
• rs12034674

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 0.306 in 152,070 control chromosomes in the GnomAD database, including 7,366 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 0.31 (7366 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0610
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.537 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: 0.306 AC: 46567 AN: 151952 Hom.: 7372 Cov.: 32

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.555

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.306 AC: 46564 AN: 152070 Hom.: 7366 Cov.: 32 AF XY: 0.305 AC XY: 22696 AN XY: 74338

African (AFR) AF: 0.339 AC: 14034 AN: 41450

American (AMR) AF: 0.290 AC: 4433 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.222 AC: 770 AN: 3472

East Asian (EAS) AF: 0.554 AC: 2851 AN: 5148

South Asian (SAS) AF: 0.320 AC: 1543 AN: 4822

European-Finnish (FIN) AF: 0.265 AC: 2807 AN: 10594

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.282 AC: 19166 AN: 67962

Other (OTH) AF: 0.307 AC: 649 AN: 2116

Alfa AF: 0.285 Hom.: 7506

Bravo AF: 0.310

Asia WGS AF: 0.423 AC: 1470 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	8.3
DANN	Benign	0.80
PhyloP100		-0.061

Splicing

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

Other links and lift over

dbSNP: rs12034674; hg19: chr1-19164527; COSMIC: COSV64744150;