2-133756869-C-T

Variant names:

• chr2-133756869-C-T
• rs4505578

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 0.72 in 152,048 control chromosomes in the GnomAD database, including 39,877 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 0.72 (39877 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 5 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 = 0.813 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: 0.719 AC: 109312 AN: 151930 Hom.: 39809 Cov.: 32

Gnomad AFR AF: 0.819

Gnomad AMI AF: 0.703

Gnomad AMR AF: 0.652

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.782

Gnomad SAS AF: 0.635

Gnomad FIN AF: 0.779

Gnomad MID AF: 0.526

Gnomad NFE AF: 0.676

Gnomad OTH AF: 0.667

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

GnomAD4 genome AF: 0.720 AC: 109445 AN: 152048 Hom.: 39877 Cov.: 32 AF XY: 0.720 AC XY: 53537 AN XY: 74324

African (AFR) AF: 0.820 AC: 34015 AN: 41490

American (AMR) AF: 0.652 AC: 9959 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.565 AC: 1959 AN: 3468

East Asian (EAS) AF: 0.782 AC: 4042 AN: 5168

South Asian (SAS) AF: 0.637 AC: 3055 AN: 4798

European-Finnish (FIN) AF: 0.779 AC: 8223 AN: 10560

Middle Eastern (MID) AF: 0.531 AC: 154 AN: 290

European-Non Finnish (NFE) AF: 0.676 AC: 45981 AN: 67980

Other (OTH) AF: 0.670 AC: 1416 AN: 2114

Alfa AF: 0.706 Hom.: 6631

Bravo AF: 0.720

Asia WGS AF: 0.716 AC: 2487 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.2
DANN	Benign	0.59
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs4505578; hg19: chr2-134514440; COSMIC: COSV107165724;