rs11564299

Variant names:

• chr18-28180064-A-G
• rs11564299
• ENST00000725545.1:n.114+1777A>G

Variant summary

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

The ENST00000725545.1(ENSG00000294740):​n.114+1777A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 152,190 control chromosomes in the GnomAD database, including 2,677 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 0.17 (2677 hom., cov: 33)
• Consequence: ENSG00000294740 ENST00000725545.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.17
• Publications: 13 publications found

Genes affected

ENSG00000294740 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.228 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
ENSG00000294740	ENST00000725545.1	n.114+1777A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25797 AN: 152072 Hom.: 2678 Cov.: 33

Gnomad AFR AF: 0.0675

Gnomad AMI AF: 0.0824

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.0296

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.170 AC: 25801 AN: 152190 Hom.: 2677 Cov.: 33 AF XY: 0.168 AC XY: 12488 AN XY: 74432

African (AFR) AF: 0.0674 AC: 2800 AN: 41552

American (AMR) AF: 0.215 AC: 3280 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 523 AN: 3468

East Asian (EAS) AF: 0.0297 AC: 154 AN: 5182

South Asian (SAS) AF: 0.145 AC: 697 AN: 4808

European-Finnish (FIN) AF: 0.211 AC: 2238 AN: 10592

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.231 AC: 15683 AN: 67982

Other (OTH) AF: 0.154 AC: 325 AN: 2114

Alfa AF: 0.207 Hom.: 2142

Bravo AF: 0.164

Asia WGS AF: 0.0900 AC: 313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	15
DANN	Benign	0.85
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs11564299; hg19: chr18-25760028;