rs2759275

Variant names:

• chr1-198075248-C-T
• rs2759275

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 0.259 in 151,810 control chromosomes in the GnomAD database, including 5,499 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 0.26 (5499 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.226
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.476 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: 0.259 AC: 39240 AN: 151692 Hom.: 5492 Cov.: 32

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.492

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.220

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.259 AC: 39270 AN: 151810 Hom.: 5499 Cov.: 32 AF XY: 0.263 AC XY: 19517 AN XY: 74188

African (AFR) AF: 0.336 AC: 13881 AN: 41366

American (AMR) AF: 0.257 AC: 3923 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.225 AC: 782 AN: 3468

East Asian (EAS) AF: 0.492 AC: 2524 AN: 5130

South Asian (SAS) AF: 0.316 AC: 1519 AN: 4808

European-Finnish (FIN) AF: 0.273 AC: 2872 AN: 10524

Middle Eastern (MID) AF: 0.233 AC: 68 AN: 292

European-Non Finnish (NFE) AF: 0.192 AC: 13074 AN: 67946

Other (OTH) AF: 0.251 AC: 530 AN: 2108

Alfa AF: 0.213 Hom.: 761

Bravo AF: 0.262

Asia WGS AF: 0.412 AC: 1431 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.8
DANN	Benign	0.53
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs2759275; hg19: chr1-198044378;