rs10485486

Variant names:

• chr20-5397506-T-C
• rs10485486
• ENST00000668553.1:n.1121-8732T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000668553.1(ENSG00000230563):​n.1121-8732T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0606 in 152,292 control chromosomes in the GnomAD database, including 356 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 0.061 (356 hom., cov: 32)
• Consequence: ENSG00000230563 ENST00000668553.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.333
• Publications: 0 publications found

Genes affected

ENSG00000230563 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.092 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000668553.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000230563	ENST00000668553.1		n.1121-8732T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0606 AC: 9229 AN: 152174 Hom.: 356 Cov.: 32

Gnomad AFR AF: 0.0160

Gnomad AMI AF: 0.0703

Gnomad AMR AF: 0.0540

Gnomad ASJ AF: 0.0279

Gnomad EAS AF: 0.000384

Gnomad SAS AF: 0.0441

Gnomad FIN AF: 0.0781

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0939

Gnomad OTH AF: 0.0635

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

GnomAD4 genome AF: 0.0606 AC: 9229 AN: 152292 Hom.: 356 Cov.: 32 AF XY: 0.0581 AC XY: 4326 AN XY: 74472

African (AFR) AF: 0.0160 AC: 664 AN: 41574

American (AMR) AF: 0.0540 AC: 825 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0279 AC: 97 AN: 3472

East Asian (EAS) AF: 0.000385 AC: 2 AN: 5190

South Asian (SAS) AF: 0.0446 AC: 215 AN: 4826

European-Finnish (FIN) AF: 0.0781 AC: 829 AN: 10616

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0939 AC: 6386 AN: 68004

Other (OTH) AF: 0.0624 AC: 132 AN: 2116

Alfa AF: 0.0782 Hom.: 425

Bravo AF: 0.0574

Asia WGS AF: 0.0170 AC: 62 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.5
DANN	Benign	0.33
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs10485486; hg19: chr20-5378152;