1-18838033-C-T

Variant names:

• chr1-18838033-C-T
• rs12034674

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 0.306 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.306 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

Gnomad4 AFR AF: 0.339

Gnomad4 AMR AF: 0.290

Gnomad4 ASJ AF: 0.222

Gnomad4 EAS AF: 0.554

Gnomad4 SAS AF: 0.320

Gnomad4 FIN AF: 0.265

Gnomad4 NFE AF: 0.282

Gnomad4 OTH AF: 0.307

Alfa AF: 0.282 Hom.: 5676

Bravo AF: 0.310

Asia WGS AF: 0.423 AC: 1470 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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