rs359980

Positions:

• chr2-218964484-T-C

Variant summary

Our verdict is Benign. Variant got -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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.457

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.218964484T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.0595

Gnomad4 ASJ AF: 0.0608

Gnomad4 EAS AF: 0.159

Gnomad4 SAS AF: 0.235

Gnomad4 FIN AF: 0.0686

Gnomad4 NFE AF: 0.0411

Gnomad4 OTH AF: 0.0767

Alfa AF: 0.0514 Hom.: 621

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs359980; hg19: chr2-219829206;