rs11081516

Variant names:

• chr18-79022312-G-A
• rs11081516
• ENST00000836199.1:n.557+1576C>T

Variant summary

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

The ENST00000836199.1(ENSG00000308736):​n.557+1576C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.436 in 152,006 control chromosomes in the GnomAD database, including 16,128 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 0.44 (16128 hom., cov: 33)
• Consequence: ENSG00000308736 ENST00000836199.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.617
• Publications: 3 publications found

Genes affected

ENSG00000308736 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.552 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372225	XR_001753513.2	n.338+1576C>T		intron_variant	Intron 2 of 2
LOC105372225	XR_001753514.2	n.226+1576C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000308736	ENST00000836199.1	n.557+1576C>T		intron_variant	Intron 2 of 2
ENSG00000308736	ENST00000836200.1	n.450+1641C>T		intron_variant	Intron 2 of 2
ENSG00000308736	ENST00000836201.1	n.531+1576C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.437 AC: 66312 AN: 151888 Hom.: 16133 Cov.: 33

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.500

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.557

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.436 AC: 66305 AN: 152006 Hom.: 16128 Cov.: 33 AF XY: 0.434 AC XY: 32234 AN XY: 74280

African (AFR) AF: 0.215 AC: 8931 AN: 41488

American (AMR) AF: 0.468 AC: 7146 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1734 AN: 3470

East Asian (EAS) AF: 0.275 AC: 1417 AN: 5152

South Asian (SAS) AF: 0.456 AC: 2195 AN: 4816

European-Finnish (FIN) AF: 0.515 AC: 5433 AN: 10546

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.557 AC: 37842 AN: 67952

Other (OTH) AF: 0.449 AC: 947 AN: 2110

Alfa AF: 0.516 Hom.: 20918

Bravo AF: 0.420

Asia WGS AF: 0.342 AC: 1192 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.41
DANN	Benign	0.61
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs11081516; hg19: chr18-76782312;