rs2186245

Variant names:

• chr1-65652381-C-T
• rs2186245

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 0.212 in 152,068 control chromosomes in the GnomAD database, including 4,568 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 (4568 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.04
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.755 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: 0.212 AC: 32174 AN: 151950 Hom.: 4566 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.0862

Gnomad EAS AF: 0.776

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.212 AC: 32195 AN: 152068 Hom.: 4568 Cov.: 32 AF XY: 0.220 AC XY: 16344 AN XY: 74314

African (AFR) AF: 0.154 AC: 6374 AN: 41524

American (AMR) AF: 0.243 AC: 3717 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0862 AC: 299 AN: 3468

East Asian (EAS) AF: 0.775 AC: 3979 AN: 5132

South Asian (SAS) AF: 0.127 AC: 612 AN: 4814

European-Finnish (FIN) AF: 0.349 AC: 3683 AN: 10556

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.191 AC: 13013 AN: 67974

Other (OTH) AF: 0.208 AC: 439 AN: 2112

Alfa AF: 0.189 Hom.: 4278

Bravo AF: 0.207

Asia WGS AF: 0.383 AC: 1329 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.2
DANN	Benign	0.15
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs2186245; hg19: chr1-66118064;