rs2018368

Variant names:

• chr11-10718819-C-G
• rs2018368
• ENST00000760187.1:n.161+10312G>C

Variant summary

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

The ENST00000760187.1(ENSG00000299059):​n.161+10312G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.594 in 151,974 control chromosomes in the GnomAD database, including 27,919 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 0.59 (27919 hom., cov: 31)
• Consequence: ENSG00000299059 ENST00000760187.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.450
• Publications: 8 publications found

Genes affected

ENSG00000299059 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.814 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
ENSG00000299059	ENST00000760187.1	n.161+10312G>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.594 AC: 90160 AN: 151854 Hom.: 27867 Cov.: 31

Gnomad AFR AF: 0.740

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.689

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.836

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.601

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

GnomAD4 genome AF: 0.594 AC: 90271 AN: 151974 Hom.: 27919 Cov.: 31 AF XY: 0.594 AC XY: 44081 AN XY: 74260

African (AFR) AF: 0.741 AC: 30697 AN: 41452

American (AMR) AF: 0.690 AC: 10543 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.556 AC: 1927 AN: 3468

East Asian (EAS) AF: 0.835 AC: 4298 AN: 5146

South Asian (SAS) AF: 0.587 AC: 2827 AN: 4820

European-Finnish (FIN) AF: 0.464 AC: 4887 AN: 10536

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.489 AC: 33259 AN: 67950

Other (OTH) AF: 0.599 AC: 1267 AN: 2116

Alfa AF: 0.538 Hom.: 2814

Bravo AF: 0.623

Asia WGS AF: 0.673 AC: 2336 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	0.62
DANN	Benign	0.43
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs2018368; hg19: chr11-10740366;