rs32934

Variant names:

• chr5-76714881-C-T
• rs32934
• ENST00000507514.1:n.39+1296G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000507514.1(ENSG00000225407):​n.39+1296G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000225407 ENST00000507514.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.280

Genes affected

ENSG00000225407 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000225407	ENST00000507514.1	n.39+1296G>A		intron_variant	Intron 1 of 3	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;