rs10485488

Variant names:

• chr20-5398902-A-G
• rs10485488
• ENST00000668553.1:n.1121-7336A>G

Your query was ambiguous. Multiple possible variants found:

• chr20-5398902-A-G
• chr20-5398902-A-T

Variant summary

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

The ENST00000668553.1(ENSG00000230563):​n.1121-7336A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 152,120 control chromosomes in the GnomAD database, including 4,350 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 0.23 (4350 hom., cov: 32)
• Consequence: ENSG00000230563 ENST00000668553.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240
• 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 (SAS) allele frequency at 95% confidence interval = 0.261 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.1121-7336A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35639 AN: 152002 Hom.: 4345 Cov.: 32

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.238

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

GnomAD4 genome AF: 0.234 AC: 35653 AN: 152120 Hom.: 4350 Cov.: 32 AF XY: 0.235 AC XY: 17490 AN XY: 74378

African (AFR) AF: 0.169 AC: 6997 AN: 41506

American (AMR) AF: 0.257 AC: 3927 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.253 AC: 876 AN: 3464

East Asian (EAS) AF: 0.222 AC: 1149 AN: 5168

South Asian (SAS) AF: 0.268 AC: 1293 AN: 4826

European-Finnish (FIN) AF: 0.244 AC: 2584 AN: 10570

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.265 AC: 17990 AN: 67986

Other (OTH) AF: 0.237 AC: 500 AN: 2110

Alfa AF: 0.255 Hom.: 5350

Bravo AF: 0.233

Asia WGS AF: 0.249 AC: 866 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.2
DANN	Benign	0.61
PhyloP100		0.24

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: rs10485488;

hg19: chr20-5379548;