chr2-218159710-CA-C

Variant names:

• chr2-218159710-CA-C
• rs11318739

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.89 (61236 hom., cov: 0)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.938 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: 0.895 AC: 136016 AN: 151990 Hom.: 61200 Cov.: 0

Gnomad AFR AF: 0.797

Gnomad AMI AF: 0.986

Gnomad AMR AF: 0.876

Gnomad ASJ AF: 0.969

Gnomad EAS AF: 0.922

Gnomad SAS AF: 0.889

Gnomad FIN AF: 0.943

Gnomad MID AF: 0.952

Gnomad NFE AF: 0.944

Gnomad OTH AF: 0.910

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

GnomAD4 genome AF: 0.895 AC: 136107 AN: 152110 Hom.: 61236 Cov.: 0 AF XY: 0.893 AC XY: 66428 AN XY: 74348

African (AFR) AF: 0.797 AC: 33001 AN: 41418

American (AMR) AF: 0.876 AC: 13397 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.969 AC: 3364 AN: 3472

East Asian (EAS) AF: 0.922 AC: 4789 AN: 5192

South Asian (SAS) AF: 0.890 AC: 4291 AN: 4824

European-Finnish (FIN) AF: 0.943 AC: 9982 AN: 10590

Middle Eastern (MID) AF: 0.949 AC: 277 AN: 292

European-Non Finnish (NFE) AF: 0.944 AC: 64180 AN: 68010

Other (OTH) AF: 0.912 AC: 1929 AN: 2116

Alfa AF: 0.912 Hom.: 7730

Bravo AF: 0.887

Asia WGS AF: 0.906 AC: 3151 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs11318739; hg19: chr2-219024433;