rs11659609

Variant names:

• chr18-78703038-G-A
• rs11659609
• ENST00000759065.1:n.185+352C>T

Variant summary

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

The ENST00000759065.1(ENSG00000298930):​n.185+352C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.281 in 152,040 control chromosomes in the GnomAD database, including 6,480 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 0.28 (6480 hom., cov: 33)
• Consequence: ENSG00000298930 ENST00000759065.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.291
• Publications: 0 publications found

Genes affected

ENSG00000298930 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.606 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
ENSG00000298930	ENST00000759065.1	n.185+352C>T		intron_variant	Intron 1 of 4
ENSG00000298930	ENST00000759067.1	n.337+352C>T		intron_variant	Intron 1 of 2
ENSG00000298930	ENST00000759068.1	n.218+352C>T		intron_variant	Intron 1 of 1
ENSG00000298930	ENST00000759069.1	n.288+352C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42749 AN: 151922 Hom.: 6477 Cov.: 33

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.339

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.624

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.226

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.281 AC: 42781 AN: 152040 Hom.: 6480 Cov.: 33 AF XY: 0.285 AC XY: 21163 AN XY: 74318

African (AFR) AF: 0.264 AC: 10959 AN: 41476

American (AMR) AF: 0.298 AC: 4549 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.231 AC: 802 AN: 3470

East Asian (EAS) AF: 0.624 AC: 3218 AN: 5154

South Asian (SAS) AF: 0.375 AC: 1807 AN: 4822

European-Finnish (FIN) AF: 0.268 AC: 2826 AN: 10564

Middle Eastern (MID) AF: 0.233 AC: 68 AN: 292

European-Non Finnish (NFE) AF: 0.260 AC: 17689 AN: 67962

Other (OTH) AF: 0.263 AC: 555 AN: 2114

Alfa AF: 0.269 Hom.: 3460

Bravo AF: 0.282

Asia WGS AF: 0.488 AC: 1693 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.6
DANN	Benign	0.79
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs11659609; hg19: chr18-76463038;