rs333856

Variant names:

• chr2-117218170-A-C
• rs333856

Your query was ambiguous. Multiple possible variants found:

• chr2-117218170-A-C
• chr2-117218170-A-G
• chr2-117218170-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.955 in 152,246 control chromosomes in the GnomAD database, including 69,504 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 0.95 (69504 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.540
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.979 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: 0.955 AC: 145242 AN: 152128 Hom.: 69469 Cov.: 33

Gnomad AFR AF: 0.888

Gnomad AMI AF: 0.997

Gnomad AMR AF: 0.966

Gnomad ASJ AF: 0.988

Gnomad EAS AF: 0.978

Gnomad SAS AF: 0.948

Gnomad FIN AF: 0.977

Gnomad MID AF: 0.981

Gnomad NFE AF: 0.985

Gnomad OTH AF: 0.968

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

GnomAD4 genome AF: 0.955 AC: 145335 AN: 152246 Hom.: 69504 Cov.: 33 AF XY: 0.955 AC XY: 71092 AN XY: 74454

African (AFR) AF: 0.888 AC: 36849 AN: 41512

American (AMR) AF: 0.966 AC: 14761 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.988 AC: 3423 AN: 3466

East Asian (EAS) AF: 0.978 AC: 5072 AN: 5184

South Asian (SAS) AF: 0.948 AC: 4578 AN: 4830

European-Finnish (FIN) AF: 0.977 AC: 10381 AN: 10620

Middle Eastern (MID) AF: 0.980 AC: 288 AN: 294

European-Non Finnish (NFE) AF: 0.985 AC: 67026 AN: 68028

Other (OTH) AF: 0.969 AC: 2050 AN: 2116

Alfa AF: 0.959 Hom.: 3636

Bravo AF: 0.952

Asia WGS AF: 0.965 AC: 3353 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.59
DANN	Benign	0.35
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs333856; hg19: chr2-117975746;