2-35318296-C-T

Variant names:

• chr2-35318296-C-T
• rs13424077

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 0.705 in 151,768 control chromosomes in the GnomAD database, including 38,851 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 0.71 (38851 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.104

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 (AFR) allele frequency at 95% confidence interval = 0.809 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: 0.705 AC: 106972 AN: 151650 Hom.: 38834 Cov.: 32

Gnomad AFR AF: 0.817

Gnomad AMI AF: 0.784

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.760

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.621

Gnomad MID AF: 0.726

Gnomad NFE AF: 0.708

Gnomad OTH AF: 0.711

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

GnomAD4 genome AF: 0.705 AC: 107037 AN: 151768 Hom.: 38851 Cov.: 32 AF XY: 0.694 AC XY: 51440 AN XY: 74164

Gnomad4 AFR AF: 0.816

Gnomad4 AMR AF: 0.649

Gnomad4 ASJ AF: 0.760

Gnomad4 EAS AF: 0.283

Gnomad4 SAS AF: 0.472

Gnomad4 FIN AF: 0.621

Gnomad4 NFE AF: 0.708

Gnomad4 OTH AF: 0.706

Alfa AF: 0.708 Hom.: 8686

Bravo AF: 0.717

Asia WGS AF: 0.435 AC: 1518 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	1.1
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13424077; hg19: chr2-35543362;