2-601905-T-G

Variant names:

• chr2-601905-T-G
• rs2867105

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;