2-145375904-C-T

Variant names:

• chr2-145375904-C-T
• rs1996286

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 0.55 in 151,918 control chromosomes in the GnomAD database, including 23,155 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 0.55 (23155 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.614
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.612 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: 0.550 AC: 83450 AN: 151800 Hom.: 23138 Cov.: 32

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.622

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.550

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.550 AC: 83510 AN: 151918 Hom.: 23155 Cov.: 32 AF XY: 0.546 AC XY: 40500 AN XY: 74218

African (AFR) AF: 0.577 AC: 23899 AN: 41438

American (AMR) AF: 0.622 AC: 9494 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.592 AC: 2056 AN: 3472

East Asian (EAS) AF: 0.550 AC: 2842 AN: 5168

South Asian (SAS) AF: 0.562 AC: 2700 AN: 4808

European-Finnish (FIN) AF: 0.427 AC: 4493 AN: 10524

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.532 AC: 36162 AN: 67934

Other (OTH) AF: 0.541 AC: 1139 AN: 2104

Alfa AF: 0.556 Hom.: 10345

Bravo AF: 0.564

Asia WGS AF: 0.554 AC: 1918 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.2
DANN	Benign	0.17
PhyloP100		0.61

Splicing

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

Other links and lift over

dbSNP: rs1996286; hg19: chr2-146133472;