rs287983

chr2-9837608-A-Cchr2-9837608-A-Gchr2-9837608-A-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 0.848 in 152,086 control chromosomes in the GnomAD database, including 55,280 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 0.85 (55280 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.480

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.92 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: 0.848 AC: 128936 AN: 151968 Hom.: 55243 Cov.: 31

Gnomad AFR AF: 0.719

Gnomad AMI AF: 0.805

Gnomad AMR AF: 0.890

Gnomad ASJ AF: 0.830

Gnomad EAS AF: 0.901

Gnomad SAS AF: 0.944

Gnomad FIN AF: 0.911

Gnomad MID AF: 0.806

Gnomad NFE AF: 0.899

Gnomad OTH AF: 0.843

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

GnomAD4 genome AF: 0.848 AC: 129033 AN: 152086 Hom.: 55280 Cov.: 31 AF XY: 0.851 AC XY: 63288 AN XY: 74342

Gnomad4 AFR AF: 0.720

Gnomad4 AMR AF: 0.890

Gnomad4 ASJ AF: 0.830

Gnomad4 EAS AF: 0.901

Gnomad4 SAS AF: 0.943

Gnomad4 FIN AF: 0.911

Gnomad4 NFE AF: 0.899

Gnomad4 OTH AF: 0.846

Alfa AF: 0.876 Hom.: 9297

Bravo AF: 0.838

Asia WGS AF: 0.919 AC: 3197 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.9
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs287983; hg19: chr2-9977737;