rs10485486

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000668553.1(ENSG00000266908):​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: ENSG00000266908 ENST00000668553.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.333

Genes affected

ENSG00000266908 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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.1121-8732T>C		intron_variant	Intron 2 of 3

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

Gnomad4 AFR AF: 0.0160

Gnomad4 AMR AF: 0.0540

Gnomad4 ASJ AF: 0.0279

Gnomad4 EAS AF: 0.000385

Gnomad4 SAS AF: 0.0446

Gnomad4 FIN AF: 0.0781

Gnomad4 NFE AF: 0.0939

Gnomad4 OTH AF: 0.0624

Alfa AF: 0.0808 Hom.: 331

Bravo AF: 0.0574

Asia WGS AF: 0.0170 AC: 62 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10485486; hg19: chr20-5378152;