rs10485487

Variant names:

• chr20-5398218-G-A
• rs10485487
• ENST00000668553.1:n.1121-8020G>A

Variant summary

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

The ENST00000668553.1(ENSG00000230563):​n.1121-8020G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 152,120 control chromosomes in the GnomAD database, including 1,208 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 0.11 (1208 hom., cov: 33)
• Consequence: ENSG00000230563 ENST00000668553.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.369
• Publications: 3 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.199 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

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000230563	ENST00000668553.1		n.1121-8020G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17171 AN: 152004 Hom.: 1207 Cov.: 33

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.0974

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.0477

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.0764

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.113 AC: 17185 AN: 152120 Hom.: 1208 Cov.: 33 AF XY: 0.114 AC XY: 8496 AN XY: 74370

African (AFR) AF: 0.174 AC: 7225 AN: 41478

American (AMR) AF: 0.116 AC: 1767 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0974 AC: 338 AN: 3470

East Asian (EAS) AF: 0.209 AC: 1082 AN: 5178

South Asian (SAS) AF: 0.161 AC: 779 AN: 4826

European-Finnish (FIN) AF: 0.0477 AC: 504 AN: 10576

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.0764 AC: 5194 AN: 67984

Other (OTH) AF: 0.120 AC: 254 AN: 2116

Alfa AF: 0.0898 Hom.: 1089

Bravo AF: 0.119

Asia WGS AF: 0.190 AC: 660 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.62
PhyloP100		0.37

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10485487;

hg19: chr20-5378864;