chr5-176520050-C-T

Position:

• chr5-176520050-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 0.49 in 152,090 control chromosomes in the GnomAD database, including 18,387 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 0.49 (18387 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.515 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.176520050C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.490 AC: 74528 AN: 151972 Hom.: 18377 Cov.: 33

Gnomad AFR AF: 0.460

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.539

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.549

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.490 AC: 74562 AN: 152090 Hom.: 18387 Cov.: 33 AF XY: 0.489 AC XY: 36373 AN XY: 74364

Gnomad4 AFR AF: 0.459

Gnomad4 AMR AF: 0.525

Gnomad4 ASJ AF: 0.539

Gnomad4 EAS AF: 0.455

Gnomad4 SAS AF: 0.399

Gnomad4 FIN AF: 0.549

Gnomad4 NFE AF: 0.497

Gnomad4 OTH AF: 0.495

Alfa AF: 0.494 Hom.: 38965

Bravo AF: 0.490

Asia WGS AF: 0.453 AC: 1575 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.033
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: rs4868644; hg19: chr5-175947051;