rs2645305

Variant names:

• chr1-119018742-A-G
• rs2645305

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 0.296 in 152,018 control chromosomes in the GnomAD database, including 7,454 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 0.30 (7454 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.484

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.441 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: 0.296 AC: 44889 AN: 151900 Hom.: 7447 Cov.: 32

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.0401

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.266

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

GnomAD4 genome AF: 0.296 AC: 44928 AN: 152018 Hom.: 7454 Cov.: 32 AF XY: 0.290 AC XY: 21539 AN XY: 74290

Gnomad4 AFR AF: 0.447

Gnomad4 AMR AF: 0.187

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.0400

Gnomad4 SAS AF: 0.251

Gnomad4 FIN AF: 0.260

Gnomad4 NFE AF: 0.260

Gnomad4 OTH AF: 0.263

Alfa AF: 0.278 Hom.: 804

Bravo AF: 0.293

Asia WGS AF: 0.181 AC: 629 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2645305; hg19: chr1-119561365; COSMIC: COSV53380863;