chr1-202937378-C-T

Variant names:

• chr1-202937378-C-T
• rs2185781

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 0.21 in 152,062 control chromosomes in the GnomAD database, including 3,499 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 0.21 (3499 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0400
• Publications: 15 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.331 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31842 AN: 151944 Hom.: 3484 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.210 AC: 31888 AN: 152062 Hom.: 3499 Cov.: 32 AF XY: 0.212 AC XY: 15729 AN XY: 74344

African (AFR) AF: 0.215 AC: 8911 AN: 41452

American (AMR) AF: 0.156 AC: 2391 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 635 AN: 3470

East Asian (EAS) AF: 0.344 AC: 1779 AN: 5172

South Asian (SAS) AF: 0.335 AC: 1616 AN: 4824

European-Finnish (FIN) AF: 0.190 AC: 2007 AN: 10558

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.206 AC: 13973 AN: 67994

Other (OTH) AF: 0.188 AC: 395 AN: 2104

Alfa AF: 0.191 Hom.: 1917

Bravo AF: 0.200

Asia WGS AF: 0.344 AC: 1195 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	14
DANN	Benign	0.78
PhyloP100		0.040

Splicing

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

Other links and lift over

dbSNP: rs2185781; hg19: chr1-202906506;