1-33463157-T-C

Variant names:

• chr1-33463157-T-C
• rs12565140

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 0.135 in 151,866 control chromosomes in the GnomAD database, including 1,864 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 0.13 (1864 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.480
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.368 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: 0.135 AC: 20486 AN: 151748 Hom.: 1866 Cov.: 30

Gnomad AFR AF: 0.0377

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.135 AC: 20479 AN: 151866 Hom.: 1864 Cov.: 30 AF XY: 0.139 AC XY: 10312 AN XY: 74182

African (AFR) AF: 0.0376 AC: 1561 AN: 41476

American (AMR) AF: 0.153 AC: 2340 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.120 AC: 415 AN: 3468

East Asian (EAS) AF: 0.382 AC: 1937 AN: 5072

South Asian (SAS) AF: 0.281 AC: 1345 AN: 4782

European-Finnish (FIN) AF: 0.159 AC: 1683 AN: 10584

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.158 AC: 10726 AN: 67922

Other (OTH) AF: 0.137 AC: 288 AN: 2102

Alfa AF: 0.144 Hom.: 3866

Bravo AF: 0.128

Asia WGS AF: 0.285 AC: 988 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.66
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs12565140; hg19: chr1-33928758; COSMIC: COSV69405507;