rs328506

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 25 publications found

Genes affected

ENSG00000286052 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.727 AC: 30128 AN: 41458

American (AMR) AF: 0.782 AC: 11949 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.726 AC: 2518 AN: 3468

East Asian (EAS) AF: 0.994 AC: 5135 AN: 5168

South Asian (SAS) AF: 0.829 AC: 3982 AN: 4804

European-Finnish (FIN) AF: 0.733 AC: 7743 AN: 10568

Middle Eastern (MID) AF: 0.726 AC: 212 AN: 292

European-Non Finnish (NFE) AF: 0.704 AC: 47820 AN: 67970

Other (OTH) AF: 0.745 AC: 1575 AN: 2114

Alfa AF: 0.722 Hom.: 88618

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
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs328506; hg19: chr20-56029604;