chr2-234306489-T-C

Position:

• chr2-234306489-T-C

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 0.47 in 151,880 control chromosomes in the GnomAD database, including 17,208 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 0.47 (17208 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00

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 (EAS) allele frequency at 95% confidence interval = 0.575 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: 0.470 AC: 71344 AN: 151762 Hom.: 17197 Cov.: 31

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.583

Gnomad ASJ AF: 0.528

Gnomad EAS AF: 0.593

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.470 AC: 71385 AN: 151880 Hom.: 17208 Cov.: 31 AF XY: 0.473 AC XY: 35145 AN XY: 74232

Gnomad4 AFR AF: 0.403

Gnomad4 AMR AF: 0.583

Gnomad4 ASJ AF: 0.528

Gnomad4 EAS AF: 0.592

Gnomad4 SAS AF: 0.468

Gnomad4 FIN AF: 0.464

Gnomad4 NFE AF: 0.475

Gnomad4 OTH AF: 0.471

Alfa AF: 0.481 Hom.: 24331

Bravo AF: 0.475

Asia WGS AF: 0.489 AC: 1699 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	6.0
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11695811; hg19: chr2-235215133;