2-1770237-C-T

Variant names:

• chr2-1770237-C-T
• rs13421140

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.266 AC: 11043 AN: 41466

American (AMR) AF: 0.158 AC: 2423 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 579 AN: 3468

East Asian (EAS) AF: 0.324 AC: 1665 AN: 5140

South Asian (SAS) AF: 0.149 AC: 718 AN: 4812

European-Finnish (FIN) AF: 0.280 AC: 2959 AN: 10564

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.226 AC: 15360 AN: 67960

Other (OTH) AF: 0.219 AC: 462 AN: 2108

Alfa AF: 0.241 Hom.: 670

Bravo AF: 0.225

Asia WGS AF: 0.213 AC: 739 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.2
DANN	Benign	0.71
PhyloP100		-0.081

Splicing

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

Other links and lift over

dbSNP: rs13421140; hg19: chr2-1774009;