2-140040174-A-G

Position:

• chr2-140040174-A-G

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 0.455 in 151,922 control chromosomes in the GnomAD database, including 16,402 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 0.45 (16402 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.07

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 (AFR) allele frequency at 95% confidence interval = 0.588 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: 0.454 AC: 68979 AN: 151804 Hom.: 16380 Cov.: 31

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.565

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.455 AC: 69053 AN: 151922 Hom.: 16402 Cov.: 31 AF XY: 0.460 AC XY: 34105 AN XY: 74218

Gnomad4 AFR AF: 0.594

Gnomad4 AMR AF: 0.425

Gnomad4 ASJ AF: 0.365

Gnomad4 EAS AF: 0.565

Gnomad4 SAS AF: 0.460

Gnomad4 FIN AF: 0.428

Gnomad4 NFE AF: 0.379

Gnomad4 OTH AF: 0.427

Alfa AF: 0.409 Hom.: 2628

Bravo AF: 0.460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.083
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1918615; hg19: chr2-140797743;