2-145375904-C-T

Position:

• chr2-145375904-C-T

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 0.55 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.614

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.145375904C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.577

Gnomad4 AMR AF: 0.622

Gnomad4 ASJ AF: 0.592

Gnomad4 EAS AF: 0.550

Gnomad4 SAS AF: 0.562

Gnomad4 FIN AF: 0.427

Gnomad4 NFE AF: 0.532

Gnomad4 OTH AF: 0.541

Alfa AF: 0.560 Hom.: 8518

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1996286; hg19: chr2-146133472;