rs32930

chr5-141733360-A-G

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, non coding transcript 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: ENST00000653358.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.714

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000653358.1	n.279-14057T>C		intron_variant, non_coding_transcript_variant

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;