rs32934

Positions:

• chr5-76714881-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 0.0722 in 152,306 control chromosomes in the GnomAD database, including 729 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 0.072 (729 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.280

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.76714881C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000225407	ENST00000507514.1	n.39+1296G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.0721 AC: 10980 AN: 152188 Hom.: 727 Cov.: 33

Gnomad AFR AF: 0.0530

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.0688

Gnomad ASJ AF: 0.0377

Gnomad EAS AF: 0.406

Gnomad SAS AF: 0.0494

Gnomad FIN AF: 0.0772

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0622

Gnomad OTH AF: 0.0793

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

GnomAD4 genome AF: 0.0722 AC: 10989 AN: 152306 Hom.: 729 Cov.: 33 AF XY: 0.0751 AC XY: 5596 AN XY: 74476

Gnomad4 AFR AF: 0.0528

Gnomad4 AMR AF: 0.0691

Gnomad4 ASJ AF: 0.0377

Gnomad4 EAS AF: 0.408

Gnomad4 SAS AF: 0.0495

Gnomad4 FIN AF: 0.0772

Gnomad4 NFE AF: 0.0622

Gnomad4 OTH AF: 0.0781

Alfa AF: 0.0607 Hom.: 155

Bravo AF: 0.0751

Asia WGS AF: 0.190 AC: 659 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	5.7
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs32934; hg19: chr5-76010706;