2-1770237-C-T

Variant names:

• chr2-1770237-C-T
• rs13421140

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 0.233 in 152,018 control chromosomes in the GnomAD database, including 4,228 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 0.23 (4228 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0810

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.311 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: 0.233 AC: 35454 AN: 151900 Hom.: 4221 Cov.: 32

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.324

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.233 AC: 35480 AN: 152018 Hom.: 4228 Cov.: 32 AF XY: 0.235 AC XY: 17465 AN XY: 74320

Gnomad4 AFR AF: 0.266

Gnomad4 AMR AF: 0.158

Gnomad4 ASJ AF: 0.167

Gnomad4 EAS AF: 0.324

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.280

Gnomad4 NFE AF: 0.226

Gnomad4 OTH AF: 0.219

Alfa AF: 0.240 Hom.: 638

Bravo AF: 0.225

Asia WGS AF: 0.213 AC: 739 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.2
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13421140; hg19: chr2-1774009;