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. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000668553.1(ENSG00000266908):​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: ENSG00000266908 ENST00000668553.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240

Genes affected

ENSG00000266908 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000266908	ENST00000668553.1	n.1121-7336A>G		intron_variant	Intron 2 of 3

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

Gnomad4 AFR AF: 0.169

Gnomad4 AMR AF: 0.257

Gnomad4 ASJ AF: 0.253

Gnomad4 EAS AF: 0.222

Gnomad4 SAS AF: 0.268

Gnomad4 FIN AF: 0.244

Gnomad4 NFE AF: 0.265

Gnomad4 OTH AF: 0.237

Alfa AF: 0.254 Hom.: 3840

Bravo AF: 0.233

Asia WGS AF: 0.249 AC: 866 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10485488; hg19: chr20-5379548;