5-2618846-C-T

Position:

• chr5-2618846-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 0.335 in 151,960 control chromosomes in the GnomAD database, including 10,023 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 0.33 (10023 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.383

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.427 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.2618846C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50830 AN: 151842 Hom.: 10016 Cov.: 31

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.429

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.461

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.335 AC: 50857 AN: 151960 Hom.: 10023 Cov.: 31 AF XY: 0.335 AC XY: 24895 AN XY: 74248

Gnomad4 AFR AF: 0.116

Gnomad4 AMR AF: 0.410

Gnomad4 ASJ AF: 0.381

Gnomad4 EAS AF: 0.360

Gnomad4 SAS AF: 0.282

Gnomad4 FIN AF: 0.461

Gnomad4 NFE AF: 0.431

Gnomad4 OTH AF: 0.325

Alfa AF: 0.393 Hom.: 3954

Bravo AF: 0.320

Asia WGS AF: 0.307 AC: 1070 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.3
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2455455; hg19: chr5-2618960;