rs11586488

Variant names:

• chr1-22022063-T-C
• rs11586488
• ENST00000648697.1:n.394-3229T>C

Variant summary

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

The ENST00000648697.1(ENSG00000285959):​n.394-3229T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 148,838 control chromosomes in the GnomAD database, including 3,951 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 0.23 (3951 hom., cov: 27)
• Consequence: ENSG00000285959 ENST00000648697.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.08
• Publications: 18 publications found

Genes affected

ENSG00000285959 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.258 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
ENSG00000285959	ENST00000648697.1	n.394-3229T>C		intron_variant	Intron 2 of 3
ENSG00000285959	ENST00000650360.1	n.1051-3229T>C		intron_variant	Intron 7 of 8

Frequencies

GnomAD3 genomes AF: 0.229 AC: 34020 AN: 148728 Hom.: 3949 Cov.: 27

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.0810

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.229 AC: 34038 AN: 148838 Hom.: 3951 Cov.: 27 AF XY: 0.227 AC XY: 16424 AN XY: 72446

African (AFR) AF: 0.201 AC: 8128 AN: 40468

American (AMR) AF: 0.265 AC: 3927 AN: 14806

Ashkenazi Jewish (ASJ) AF: 0.254 AC: 878 AN: 3452

East Asian (EAS) AF: 0.107 AC: 512 AN: 4796

South Asian (SAS) AF: 0.0822 AC: 378 AN: 4600

European-Finnish (FIN) AF: 0.253 AC: 2567 AN: 10128

Middle Eastern (MID) AF: 0.319 AC: 88 AN: 276

European-Non Finnish (NFE) AF: 0.249 AC: 16753 AN: 67366

Other (OTH) AF: 0.231 AC: 475 AN: 2054

Alfa AF: 0.240 Hom.: 706

Bravo AF: 0.228

Asia WGS AF: 0.113 AC: 394 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.16
DANN	Benign	0.26
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs11586488; hg19: chr1-22348556;