rs10485487

chr20-5398218-G-A

Variant summary

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

The ENST00000668553.1(ENSG00000266908):n.1121-8020G>A variant causes a intron, non coding transcript 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: ENST00000668553.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.369

Genes affected

(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 (EAS) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000668553.1	n.1121-8020G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.174

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.0974

Gnomad4 EAS AF: 0.209

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.0477

Gnomad4 NFE AF: 0.0764

Gnomad4 OTH AF: 0.120

Alfa AF: 0.0827 Hom.: 568

Bravo AF: 0.119

Asia WGS AF: 0.190 AC: 660 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.0
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10485487; hg19: chr20-5378864;