2-197341116-C-A

Variant names:

• chr2-197341116-C-A
• rs12472355

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 0.388 in 151,932 control chromosomes in the GnomAD database, including 11,899 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 0.39 (11899 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.937

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 (AFR) allele frequency at 95% confidence interval = 0.469 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: 0.388 AC: 58922 AN: 151814 Hom.: 11874 Cov.: 31

Gnomad AFR AF: 0.474

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.465

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.194

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.388 AC: 58986 AN: 151932 Hom.: 11899 Cov.: 31 AF XY: 0.389 AC XY: 28886 AN XY: 74270

Gnomad4 AFR AF: 0.474

Gnomad4 AMR AF: 0.397

Gnomad4 ASJ AF: 0.267

Gnomad4 EAS AF: 0.464

Gnomad4 SAS AF: 0.304

Gnomad4 FIN AF: 0.444

Gnomad4 NFE AF: 0.335

Gnomad4 OTH AF: 0.357

Alfa AF: 0.318 Hom.: 3615

Bravo AF: 0.395

Asia WGS AF: 0.398 AC: 1381 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	0.73
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12472355; hg19: chr2-198205840;