chr5-75335314-C-T

Position:

• chr5-75335314-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 0.0817 in 152,270 control chromosomes in the GnomAD database, including 595 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 0.082 (595 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0530

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.113 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.75335314C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000247372	ENST00000501886.2	n.107-276G>A		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.0818 AC: 12441 AN: 152152 Hom.: 594 Cov.: 32

Gnomad AFR AF: 0.0326

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.0275

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0976

Gnomad OTH AF: 0.0708

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

GnomAD4 genome AF: 0.0817 AC: 12437 AN: 152270 Hom.: 595 Cov.: 32 AF XY: 0.0830 AC XY: 6178 AN XY: 74456

Gnomad4 AFR AF: 0.0325

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.165

Gnomad4 EAS AF: 0.0270

Gnomad4 SAS AF: 0.121

Gnomad4 FIN AF: 0.111

Gnomad4 NFE AF: 0.0976

Gnomad4 OTH AF: 0.0701

Alfa AF: 0.0950 Hom.: 719

Bravo AF: 0.0765

Asia WGS AF: 0.0750 AC: 261 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.93
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3761738; hg19: chr5-74631139;