2-201099723-C-T

Variant names:

• chr2-201099723-C-T
• rs12470378

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 0.0201 in 152,212 control chromosomes in the GnomAD database, including 251 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 0.020 (251 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.14

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.243 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: 0.0200 AC: 3046 AN: 152094 Hom.: 248 Cov.: 31

Gnomad AFR AF: 0.00396

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0886

Gnomad ASJ AF: 0.00720

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.00993

Gnomad FIN AF: 0.00311

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000838

Gnomad OTH AF: 0.0239

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

GnomAD4 genome AF: 0.0201 AC: 3058 AN: 152212 Hom.: 251 Cov.: 31 AF XY: 0.0226 AC XY: 1683 AN XY: 74430

Gnomad4 AFR AF: 0.00395

Gnomad4 AMR AF: 0.0896

Gnomad4 ASJ AF: 0.00720

Gnomad4 EAS AF: 0.254

Gnomad4 SAS AF: 0.00973

Gnomad4 FIN AF: 0.00311

Gnomad4 NFE AF: 0.000838

Gnomad4 OTH AF: 0.0237

Alfa AF: 0.00971 Hom.: 119

Bravo AF: 0.0289

Asia WGS AF: 0.0960 AC: 333 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	14
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12470378; hg19: chr2-201964446;