2-117516426-T-C

Position:

• chr2-117516426-T-C

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 0.85 in 152,094 control chromosomes in the GnomAD database, including 55,156 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 0.85 (55156 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0680

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.117516426T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.850 AC: 129167 AN: 151976 Hom.: 55107 Cov.: 32

Gnomad AFR AF: 0.795

Gnomad AMI AF: 0.675

Gnomad AMR AF: 0.892

Gnomad ASJ AF: 0.906

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.930

Gnomad FIN AF: 0.851

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.856

Gnomad OTH AF: 0.858

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

GnomAD4 genome AF: 0.850 AC: 129271 AN: 152094 Hom.: 55156 Cov.: 32 AF XY: 0.851 AC XY: 63287 AN XY: 74360

Gnomad4 AFR AF: 0.795

Gnomad4 AMR AF: 0.893

Gnomad4 ASJ AF: 0.906

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.930

Gnomad4 FIN AF: 0.851

Gnomad4 NFE AF: 0.856

Gnomad4 OTH AF: 0.860

Alfa AF: 0.859 Hom.: 75402

Bravo AF: 0.850

Asia WGS AF: 0.954 AC: 3313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.5
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4849561; hg19: chr2-118274002;