2-55865477-C-T

Position:

• chr2-55865477-C-T

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 0.658 in 151,910 control chromosomes in the GnomAD database, including 34,628 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 0.66 (34628 hom., cov: 30)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.137

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.876 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.55865477C>T		intergenic_region
LOC112268416	XR_002959388.2	n.229-8406C>T		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.657 AC: 99791 AN: 151792 Hom.: 34587 Cov.: 30

Gnomad AFR AF: 0.860

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.538

Gnomad ASJ AF: 0.737

Gnomad EAS AF: 0.897

Gnomad SAS AF: 0.677

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.670

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

GnomAD4 genome AF: 0.658 AC: 99890 AN: 151910 Hom.: 34628 Cov.: 30 AF XY: 0.654 AC XY: 48558 AN XY: 74224

Gnomad4 AFR AF: 0.860

Gnomad4 AMR AF: 0.538

Gnomad4 ASJ AF: 0.737

Gnomad4 EAS AF: 0.897

Gnomad4 SAS AF: 0.678

Gnomad4 FIN AF: 0.440

Gnomad4 NFE AF: 0.569

Gnomad4 OTH AF: 0.673

Alfa AF: 0.585 Hom.: 35532

Bravo AF: 0.671

Asia WGS AF: 0.784 AC: 2728 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.1
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1346787; hg19: chr2-56092612;