1-33463157-T-C

Position:

• chr1-33463157-T-C

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 0.135 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.0376

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.120

Gnomad4 EAS AF: 0.382

Gnomad4 SAS AF: 0.281

Gnomad4 FIN AF: 0.159

Gnomad4 NFE AF: 0.158

Gnomad4 OTH AF: 0.137

Alfa AF: 0.152 Hom.: 2630

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

Splicing

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

Publications

LitVar

Other links and lift over

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