2-235216378-C-T

Variant names:

• chr2-235216378-C-T
• rs2060127

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 0.727 in 152,090 control chromosomes in the GnomAD database, including 40,881 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 0.73 (40881 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.45

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.895 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: 0.727 AC: 110462 AN: 151972 Hom.: 40840 Cov.: 32

Gnomad AFR AF: 0.592

Gnomad AMI AF: 0.693

Gnomad AMR AF: 0.704

Gnomad ASJ AF: 0.766

Gnomad EAS AF: 0.917

Gnomad SAS AF: 0.860

Gnomad FIN AF: 0.778

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.781

Gnomad OTH AF: 0.737

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

GnomAD4 genome AF: 0.727 AC: 110559 AN: 152090 Hom.: 40881 Cov.: 32 AF XY: 0.729 AC XY: 54178 AN XY: 74360

Gnomad4 AFR AF: 0.592

Gnomad4 AMR AF: 0.704

Gnomad4 ASJ AF: 0.766

Gnomad4 EAS AF: 0.917

Gnomad4 SAS AF: 0.860

Gnomad4 FIN AF: 0.778

Gnomad4 NFE AF: 0.781

Gnomad4 OTH AF: 0.740

Alfa AF: 0.739 Hom.: 7071

Bravo AF: 0.715

Asia WGS AF: 0.874 AC: 3037 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.020
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2060127; hg19: chr2-236125022;