11-18800490-A-G

Variant names:

• chr11-18800490-A-G
• rs4627050
• ENST00000836338.1:n.162+9557A>G

Variant summary

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

The ENST00000836338.1(ENSG00000255244):​n.162+9557A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.611 in 152,020 control chromosomes in the GnomAD database, including 28,483 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 0.61 (28483 hom., cov: 31)
• Consequence: ENSG00000255244 ENST00000836338.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502
• Publications: 6 publications found

Genes affected

ENSG00000255244 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.733 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
ENSG00000255244	ENST00000836338.1	n.162+9557A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.611 AC: 92766 AN: 151902 Hom.: 28456 Cov.: 31

Gnomad AFR AF: 0.562

Gnomad AMI AF: 0.667

Gnomad AMR AF: 0.652

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.736

Gnomad SAS AF: 0.753

Gnomad FIN AF: 0.619

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.611

Gnomad OTH AF: 0.582

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

GnomAD4 genome AF: 0.611 AC: 92835 AN: 152020 Hom.: 28483 Cov.: 31 AF XY: 0.615 AC XY: 45725 AN XY: 74292

African (AFR) AF: 0.562 AC: 23275 AN: 41444

American (AMR) AF: 0.652 AC: 9963 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.593 AC: 2056 AN: 3468

East Asian (EAS) AF: 0.735 AC: 3790 AN: 5156

South Asian (SAS) AF: 0.753 AC: 3628 AN: 4818

European-Finnish (FIN) AF: 0.619 AC: 6543 AN: 10566

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.612 AC: 41577 AN: 67984

Other (OTH) AF: 0.587 AC: 1237 AN: 2106

Alfa AF: 0.610 Hom.: 57681

Bravo AF: 0.609

Asia WGS AF: 0.756 AC: 2629 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.32
DANN	Benign	0.34
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs4627050; hg19: chr11-18822037; COSMIC: COSV73894423;