rs10485747

Variant names:

• chr20-11324543-T-C
• rs10485747
• ENST00000784589.1:n.570-11383A>G

Variant summary

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

The ENST00000784589.1(ENSG00000302131):​n.570-11383A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 152,158 control chromosomes in the GnomAD database, including 4,121 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 0.22 (4121 hom., cov: 33)
• Consequence: ENSG00000302131 ENST00000784589.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.753
• Publications: 3 publications found

Genes affected

ENSG00000302131 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372529	XR_937261.2	n.552-11383A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302131	ENST00000784589.1	n.570-11383A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.217 AC: 32961 AN: 152040 Hom.: 4118 Cov.: 33

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.217 AC: 32979 AN: 152158 Hom.: 4121 Cov.: 33 AF XY: 0.215 AC XY: 16023 AN XY: 74380

African (AFR) AF: 0.104 AC: 4336 AN: 41544

American (AMR) AF: 0.239 AC: 3648 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.271 AC: 941 AN: 3472

East Asian (EAS) AF: 0.448 AC: 2306 AN: 5150

South Asian (SAS) AF: 0.346 AC: 1669 AN: 4824

European-Finnish (FIN) AF: 0.182 AC: 1926 AN: 10580

Middle Eastern (MID) AF: 0.271 AC: 79 AN: 292

European-Non Finnish (NFE) AF: 0.255 AC: 17338 AN: 67996

Other (OTH) AF: 0.229 AC: 485 AN: 2114

Alfa AF: 0.253 Hom.: 8895

Bravo AF: 0.220

Asia WGS AF: 0.387 AC: 1345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	9.1
DANN	Benign	0.44
PhyloP100		0.75

Splicing

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

Other links and lift over

dbSNP: rs10485747; hg19: chr20-11305191;