2-42894144-T-G

Variant names:

• chr2-42894144-T-G
• rs4953675

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 0.829 in 151,994 control chromosomes in the GnomAD database, including 52,884 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 0.83 (52884 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.274

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.949 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: 0.829 AC: 125851 AN: 151876 Hom.: 52811 Cov.: 29

Gnomad AFR AF: 0.957

Gnomad AMI AF: 0.621

Gnomad AMR AF: 0.857

Gnomad ASJ AF: 0.834

Gnomad EAS AF: 0.654

Gnomad SAS AF: 0.902

Gnomad FIN AF: 0.737

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.769

Gnomad OTH AF: 0.827

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

GnomAD4 genome AF: 0.829 AC: 125983 AN: 151994 Hom.: 52884 Cov.: 29 AF XY: 0.827 AC XY: 61420 AN XY: 74272

Gnomad4 AFR AF: 0.957

Gnomad4 AMR AF: 0.857

Gnomad4 ASJ AF: 0.834

Gnomad4 EAS AF: 0.654

Gnomad4 SAS AF: 0.904

Gnomad4 FIN AF: 0.737

Gnomad4 NFE AF: 0.769

Gnomad4 OTH AF: 0.830

Alfa AF: 0.789 Hom.: 21285

Bravo AF: 0.843

Asia WGS AF: 0.816 AC: 2837 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.1
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4953675; hg19: chr2-43121284;