chr5-75742893-C-G

Position:

• chr5-75742893-C-G

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 0.555 in 151,842 control chromosomes in the GnomAD database, including 23,988 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 0.56 (23988 hom., cov: 30)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0460

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.623 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.75742893C>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.555 AC: 84268 AN: 151724 Hom.: 23980 Cov.: 30

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.494

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.578

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.628

Gnomad OTH AF: 0.596

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

GnomAD4 genome AF: 0.555 AC: 84320 AN: 151842 Hom.: 23988 Cov.: 30 AF XY: 0.554 AC XY: 41082 AN XY: 74222

Gnomad4 AFR AF: 0.421

Gnomad4 AMR AF: 0.578

Gnomad4 ASJ AF: 0.576

Gnomad4 EAS AF: 0.495

Gnomad4 SAS AF: 0.590

Gnomad4 FIN AF: 0.578

Gnomad4 NFE AF: 0.628

Gnomad4 OTH AF: 0.598

Alfa AF: 0.471 Hom.: 1438

Bravo AF: 0.550

Asia WGS AF: 0.553 AC: 1925 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.86
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs258494; hg19: chr5-75038718;