rs10485546

Variant names:

• chr20-16059682-C-T
• rs10485546
• ENST00000721848.1:n.361+178G>A

Variant summary

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

The ENST00000721848.1(ENSG00000294201):​n.361+178G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0238 in 113,130 control chromosomes in the GnomAD database, including 48 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 0.024 (48 hom., cov: 29)
• Consequence: ENSG00000294201 ENST00000721848.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.953
• Publications: 1 publications found

Genes affected

ENSG00000294201 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0922 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
ENSG00000294201	ENST00000721848.1	n.361+178G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0239 AC: 2697 AN: 113054 Hom.: 48 Cov.: 29

Gnomad AFR AF: 0.00840

Gnomad AMI AF: 0.0375

Gnomad AMR AF: 0.0257

Gnomad ASJ AF: 0.00802

Gnomad EAS AF: 0.0997

Gnomad SAS AF: 0.0290

Gnomad FIN AF: 0.0469

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0204

Gnomad OTH AF: 0.0202

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

GnomAD4 genome AF: 0.0238 AC: 2697 AN: 113130 Hom.: 48 Cov.: 29 AF XY: 0.0252 AC XY: 1411 AN XY: 56032

African (AFR) AF: 0.00838 AC: 219 AN: 26140

American (AMR) AF: 0.0260 AC: 324 AN: 12480

Ashkenazi Jewish (ASJ) AF: 0.00802 AC: 22 AN: 2744

East Asian (EAS) AF: 0.0993 AC: 514 AN: 5174

South Asian (SAS) AF: 0.0288 AC: 133 AN: 4618

European-Finnish (FIN) AF: 0.0469 AC: 385 AN: 8202

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 266

European-Non Finnish (NFE) AF: 0.0204 AC: 1045 AN: 51284

Other (OTH) AF: 0.0199 AC: 32 AN: 1608

Alfa AF: 0.0186 Hom.: 26

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.40
DANN	Benign	0.56
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs10485546; hg19: chr20-16040327;