rs328506

Variant names:

• chr20-57454548-T-C
• rs328506
• ENST00000652193.1:n.409-2544T>C

Variant summary

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

The ENST00000652193.1(ENSG00000286052):​n.409-2544T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.735 in 152,028 control chromosomes in the GnomAD database, including 41,290 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 0.74 (41290 hom., cov: 31)
• Consequence: ENSG00000286052 ENST00000652193.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.339

Genes affected

ENSG00000286052 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.971 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
ENSG00000286052	ENST00000652193.1	n.409-2544T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.735 AC: 111670 AN: 151910 Hom.: 41248 Cov.: 31

Gnomad AFR AF: 0.727

Gnomad AMI AF: 0.776

Gnomad AMR AF: 0.782

Gnomad ASJ AF: 0.726

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.829

Gnomad FIN AF: 0.733

Gnomad MID AF: 0.742

Gnomad NFE AF: 0.704

Gnomad OTH AF: 0.742

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

GnomAD4 genome AF: 0.735 AC: 111770 AN: 152028 Hom.: 41290 Cov.: 31 AF XY: 0.739 AC XY: 54898 AN XY: 74300

Gnomad4 AFR AF: 0.727

Gnomad4 AMR AF: 0.782

Gnomad4 ASJ AF: 0.726

Gnomad4 EAS AF: 0.994

Gnomad4 SAS AF: 0.829

Gnomad4 FIN AF: 0.733

Gnomad4 NFE AF: 0.704

Gnomad4 OTH AF: 0.745

Alfa AF: 0.716 Hom.: 52371

Bravo AF: 0.740

Asia WGS AF: 0.917 AC: 3188 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs328506; hg19: chr20-56029604;