rs888351

Variant names:

• chr2-64799195-T-A
• rs888351

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 0.926 in 152,238 control chromosomes in the GnomAD database, including 65,318 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 0.93 (65318 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.125

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.953 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: 0.926 AC: 140826 AN: 152120 Hom.: 65266 Cov.: 31

Gnomad AFR AF: 0.961

Gnomad AMI AF: 0.843

Gnomad AMR AF: 0.945

Gnomad ASJ AF: 0.961

Gnomad EAS AF: 0.913

Gnomad SAS AF: 0.970

Gnomad FIN AF: 0.850

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.908

Gnomad OTH AF: 0.939

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

GnomAD4 genome AF: 0.926 AC: 140937 AN: 152238 Hom.: 65318 Cov.: 31 AF XY: 0.924 AC XY: 68768 AN XY: 74414

Gnomad4 AFR AF: 0.961

Gnomad4 AMR AF: 0.945

Gnomad4 ASJ AF: 0.961

Gnomad4 EAS AF: 0.914

Gnomad4 SAS AF: 0.970

Gnomad4 FIN AF: 0.850

Gnomad4 NFE AF: 0.908

Gnomad4 OTH AF: 0.939

Alfa AF: 0.902 Hom.: 3391

Bravo AF: 0.933

Asia WGS AF: 0.949 AC: 3298 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	3.7
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs888351; hg19: chr2-65026329;