rs2645305

Positions:

• chr1-119018742-A-G

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;