rs1808458

chr2-118121677-C-T

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 0.0741 in 152,186 control chromosomes in the GnomAD database, including 525 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 0.074 (525 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0150

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0738 AC: 11226 AN: 152070 Hom.: 514 Cov.: 33

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.0604

Gnomad ASJ AF: 0.0513

Gnomad EAS AF: 0.0210

Gnomad SAS AF: 0.0480

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0565

Gnomad OTH AF: 0.0592

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

GnomAD4 genome AF: 0.0741 AC: 11270 AN: 152186 Hom.: 525 Cov.: 33 AF XY: 0.0761 AC XY: 5663 AN XY: 74412

Gnomad4 AFR AF: 0.105

Gnomad4 AMR AF: 0.0605

Gnomad4 ASJ AF: 0.0513

Gnomad4 EAS AF: 0.0208

Gnomad4 SAS AF: 0.0481

Gnomad4 FIN AF: 0.128

Gnomad4 NFE AF: 0.0565

Gnomad4 OTH AF: 0.0662

Alfa AF: 0.0616 Hom.: 196

Bravo AF: 0.0728

Asia WGS AF: 0.0610 AC: 211 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.1
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1808458; hg19: chr2-118879253; COSMIC: COSV60100177;