rs32930

Variant names:

• chr5-141733360-A-G
• rs32930
• ENST00000653358.1:n.279-14057T>C

Variant summary

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

The ENST00000653358.1(ENSG00000286736):​n.279-14057T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.431 in 151,960 control chromosomes in the GnomAD database, including 15,546 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 0.43 (15546 hom., cov: 31)
• Consequence: ENSG00000286736 ENST00000653358.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.714

Genes affected

ENSG00000286736 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.671 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
ENSG00000286736	ENST00000653358.1	n.279-14057T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65516 AN: 151844 Hom.: 15546 Cov.: 31

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.463

Gnomad EAS AF: 0.690

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.429

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

GnomAD4 genome AF: 0.431 AC: 65525 AN: 151960 Hom.: 15546 Cov.: 31 AF XY: 0.431 AC XY: 32006 AN XY: 74262

Gnomad4 AFR AF: 0.227

Gnomad4 AMR AF: 0.380

Gnomad4 ASJ AF: 0.463

Gnomad4 EAS AF: 0.690

Gnomad4 SAS AF: 0.586

Gnomad4 FIN AF: 0.512

Gnomad4 NFE AF: 0.524

Gnomad4 OTH AF: 0.437

Alfa AF: 0.499 Hom.: 25491

Bravo AF: 0.411

Asia WGS AF: 0.623 AC: 2167 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.76
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs32930; hg19: chr5-141112927;