1-202937378-C-T

Variant names:

• chr1-202937378-C-T
• rs2185781

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 0.21 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.210 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

Gnomad4 AFR AF: 0.215

Gnomad4 AMR AF: 0.156

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.344

Gnomad4 SAS AF: 0.335

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.206

Gnomad4 OTH AF: 0.188

Alfa AF: 0.190 Hom.: 1755

Bravo AF: 0.200

Asia WGS AF: 0.344 AC: 1195 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2185781; hg19: chr1-202906506;