2-1770237-C-T

Position:

• chr2-1770237-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;