rs359980

Variant names:

• chr2-218964484-T-C
• rs359980

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.0786 in 152,248 control chromosomes in the GnomAD database, including 636 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 0.079 (636 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.457
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.41).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.224 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: 0.0786 AC: 11959 AN: 152130 Hom.: 637 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.0597

Gnomad ASJ AF: 0.0608

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.0686

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0411

Gnomad OTH AF: 0.0732

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

GnomAD4 genome AF: 0.0786 AC: 11971 AN: 152248 Hom.: 636 Cov.: 32 AF XY: 0.0823 AC XY: 6124 AN XY: 74438

African (AFR) AF: 0.123 AC: 5106 AN: 41516

American (AMR) AF: 0.0595 AC: 911 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0608 AC: 211 AN: 3472

East Asian (EAS) AF: 0.159 AC: 825 AN: 5180

South Asian (SAS) AF: 0.235 AC: 1136 AN: 4826

European-Finnish (FIN) AF: 0.0686 AC: 728 AN: 10608

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0411 AC: 2796 AN: 68022

Other (OTH) AF: 0.0767 AC: 162 AN: 2112

Alfa AF: 0.0536 Hom.: 1328

Bravo AF: 0.0772

Asia WGS AF: 0.200 AC: 695 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.41
CADD	Benign	17
DANN	Benign	0.81
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs359980; hg19: chr2-219829206;