rs11872889

Variant names:

• chr18-60350190-G-A
• rs11872889
• ENST00000650201.1:n.113+20845G>A

Variant summary

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

The ENST00000650201.1(ENSG00000285681):​n.113+20845G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0352 in 152,240 control chromosomes in the GnomAD database, including 142 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 0.035 (142 hom., cov: 32)
• Consequence: ENSG00000285681 ENST00000650201.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0700
• Publications: 2 publications found

Genes affected

ENSG00000285681 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0545 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650201.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285681	ENST00000650201.1		n.113+20845G>A		intron	N/A
	ENSG00000285681	ENST00000658928.1		n.156+20845G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0352 AC: 5358 AN: 152122 Hom.: 142 Cov.: 32

Gnomad AFR AF: 0.00956

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.0365

Gnomad ASJ AF: 0.0643

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.00580

Gnomad FIN AF: 0.0188

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0560

Gnomad OTH AF: 0.0474

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

GnomAD4 genome AF: 0.0352 AC: 5355 AN: 152240 Hom.: 142 Cov.: 32 AF XY: 0.0319 AC XY: 2378 AN XY: 74444

African (AFR) AF: 0.00951 AC: 395 AN: 41542

American (AMR) AF: 0.0364 AC: 556 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0643 AC: 223 AN: 3468

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5178

South Asian (SAS) AF: 0.00581 AC: 28 AN: 4820

European-Finnish (FIN) AF: 0.0188 AC: 199 AN: 10608

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

European-Non Finnish (NFE) AF: 0.0560 AC: 3808 AN: 68016

Other (OTH) AF: 0.0469 AC: 99 AN: 2110

Alfa AF: 0.0499 Hom.: 290

Bravo AF: 0.0362

Asia WGS AF: 0.00751 AC: 26 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.8
DANN	Benign	0.75
PhyloP100		0.070

Splicing

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

Other links and lift over

dbSNP: rs11872889; hg19: chr18-58017423;