1-53492930-C-T

Variant names:

• chr1-53492930-C-T
• rs1298637

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 0.443 in 152,184 control chromosomes in the GnomAD database, including 20,142 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 0.44 (20142 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.85 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: 0.442 AC: 67278 AN: 152064 Hom.: 20087 Cov.: 33

Gnomad AFR AF: 0.857

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.322

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.443 AC: 67391 AN: 152184 Hom.: 20142 Cov.: 33 AF XY: 0.438 AC XY: 32583 AN XY: 74392

African (AFR) AF: 0.857 AC: 35593 AN: 41516

American (AMR) AF: 0.275 AC: 4211 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.266 AC: 924 AN: 3470

East Asian (EAS) AF: 0.500 AC: 2590 AN: 5178

South Asian (SAS) AF: 0.424 AC: 2042 AN: 4818

European-Finnish (FIN) AF: 0.245 AC: 2601 AN: 10598

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.270 AC: 18374 AN: 67998

Other (OTH) AF: 0.402 AC: 850 AN: 2114

Alfa AF: 0.320 Hom.: 7142

Bravo AF: 0.460

Asia WGS AF: 0.482 AC: 1678 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.20
DANN	Benign	0.55
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1298637; hg19: chr1-53958603; COSMIC: COSV63362725;