rs1567868

chr2-218161896-G-Achr2-218161896-G-Cchr2-218161896-G-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 0.88 in 150,830 control chromosomes in the GnomAD database, including 59,410 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 0.88 (59410 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.937 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: 0.880 AC: 132690 AN: 150714 Hom.: 59381 Cov.: 30

Gnomad AFR AF: 0.747

Gnomad AMI AF: 0.986

Gnomad AMR AF: 0.872

Gnomad ASJ AF: 0.968

Gnomad EAS AF: 0.922

Gnomad SAS AF: 0.848

Gnomad FIN AF: 0.942

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.943

Gnomad OTH AF: 0.907

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

GnomAD4 genome AF: 0.880 AC: 132771 AN: 150830 Hom.: 59410 Cov.: 30 AF XY: 0.879 AC XY: 64762 AN XY: 73694

Gnomad4 AFR AF: 0.747

Gnomad4 AMR AF: 0.872

Gnomad4 ASJ AF: 0.968

Gnomad4 EAS AF: 0.922

Gnomad4 SAS AF: 0.849

Gnomad4 FIN AF: 0.942

Gnomad4 NFE AF: 0.943

Gnomad4 OTH AF: 0.909

Alfa AF: 0.879 Hom.: 8781

Bravo AF: 0.871

Asia WGS AF: 0.883 AC: 3073 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.39
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1567868; hg19: chr2-219026619;