2-601905-T-G

Position:

• chr2-601905-T-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 0.841 in 152,250 control chromosomes in the GnomAD database, including 54,047 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 0.84 (54047 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.635

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 (EAS) allele frequency at 95% confidence interval = 0.898 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: 0.841 AC: 127971 AN: 152132 Hom.: 54011 Cov.: 33

Gnomad AFR AF: 0.876

Gnomad AMI AF: 0.836

Gnomad AMR AF: 0.866

Gnomad ASJ AF: 0.724

Gnomad EAS AF: 0.919

Gnomad SAS AF: 0.746

Gnomad FIN AF: 0.846

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.821

Gnomad OTH AF: 0.833

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

GnomAD4 genome AF: 0.841 AC: 128062 AN: 152250 Hom.: 54047 Cov.: 33 AF XY: 0.843 AC XY: 62724 AN XY: 74420

Gnomad4 AFR AF: 0.876

Gnomad4 AMR AF: 0.866

Gnomad4 ASJ AF: 0.724

Gnomad4 EAS AF: 0.919

Gnomad4 SAS AF: 0.744

Gnomad4 FIN AF: 0.846

Gnomad4 NFE AF: 0.821

Gnomad4 OTH AF: 0.834

Alfa AF: 0.819 Hom.: 67731

Bravo AF: 0.846

Asia WGS AF: 0.861 AC: 2994 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.4
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2867105; hg19: chr2-601905;