chr2-203835966-C-T

Variant names:

• chr2-203835966-C-T
• rs12990970

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 0.379 in 151,930 control chromosomes in the GnomAD database, including 11,310 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 0.38 (11310 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0460

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.575 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: 0.379 AC: 57591 AN: 151812 Hom.: 11313 Cov.: 31

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.529

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.379 AC: 57596 AN: 151930 Hom.: 11310 Cov.: 31 AF XY: 0.377 AC XY: 27970 AN XY: 74276

Gnomad4 AFR AF: 0.301

Gnomad4 AMR AF: 0.413

Gnomad4 ASJ AF: 0.501

Gnomad4 EAS AF: 0.245

Gnomad4 SAS AF: 0.593

Gnomad4 FIN AF: 0.309

Gnomad4 NFE AF: 0.416

Gnomad4 OTH AF: 0.436

Alfa AF: 0.390 Hom.: 1486

Bravo AF: 0.378

Asia WGS AF: 0.447 AC: 1556 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.4
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12990970; hg19: chr2-204700689;