rs2353169

Variant names:

• chr1-5236784-T-C
• rs2353169

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 0.332 in 152,052 control chromosomes in the GnomAD database, including 10,258 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 0.33 (10258 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.45 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: 0.332 AC: 50455 AN: 151934 Hom.: 10256 Cov.: 32

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.332 AC: 50455 AN: 152052 Hom.: 10258 Cov.: 32 AF XY: 0.331 AC XY: 24612 AN XY: 74336

African (AFR) AF: 0.103 AC: 4261 AN: 41500

American (AMR) AF: 0.320 AC: 4880 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.436 AC: 1513 AN: 3470

East Asian (EAS) AF: 0.244 AC: 1265 AN: 5174

South Asian (SAS) AF: 0.237 AC: 1144 AN: 4820

European-Finnish (FIN) AF: 0.488 AC: 5149 AN: 10546

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.454 AC: 30864 AN: 67960

Other (OTH) AF: 0.377 AC: 797 AN: 2114

Alfa AF: 0.406 Hom.: 42337

Bravo AF: 0.315

Asia WGS AF: 0.227 AC: 790 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.0040
DANN	Benign	0.29
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs2353169; hg19: chr1-5296844;