rs1503420

Variant names:

• chr11-121695189-G-A
• rs1503420
• ENST00000652518.1:n.139+20790G>A

Variant summary

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

The ENST00000652518.1(ENSG00000286044):​n.139+20790G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,104 control chromosomes in the GnomAD database, including 2,284 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 (2284 hom., cov: 32)
• Consequence: ENSG00000286044 ENST00000652518.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.422
• Publications: 5 publications found

Genes affected

ENSG00000286044 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.324 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
ENSG00000286044	ENST00000652518.1	n.139+20790G>A		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16158 AN: 151986 Hom.: 2281 Cov.: 32

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0459

Gnomad ASJ AF: 0.00835

Gnomad EAS AF: 0.0364

Gnomad SAS AF: 0.00540

Gnomad FIN AF: 0.0404

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0149

Gnomad OTH AF: 0.0873

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

GnomAD4 genome AF: 0.107 AC: 16205 AN: 152104 Hom.: 2284 Cov.: 32 AF XY: 0.104 AC XY: 7737 AN XY: 74364

African (AFR) AF: 0.328 AC: 13616 AN: 41458

American (AMR) AF: 0.0458 AC: 700 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.00835 AC: 29 AN: 3472

East Asian (EAS) AF: 0.0363 AC: 188 AN: 5184

South Asian (SAS) AF: 0.00540 AC: 26 AN: 4812

European-Finnish (FIN) AF: 0.0404 AC: 428 AN: 10586

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0149 AC: 1016 AN: 68002

Other (OTH) AF: 0.0874 AC: 184 AN: 2106

Alfa AF: 0.0561 Hom.: 419

Bravo AF: 0.120

Asia WGS AF: 0.0500 AC: 173 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.8
DANN	Benign	0.50
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs1503420; hg19: chr11-121565897;