chr18-28773760-A-G

Variant names:

• chr18-28773760-A-G
• rs11083301
• ENST00000649159.1:n.217-15114A>G

Variant summary

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

The ENST00000649159.1(ENSG00000265994):​n.217-15114A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.415 in 151,832 control chromosomes in the GnomAD database, including 15,457 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 0.41 (15457 hom., cov: 32)
• Consequence: ENSG00000265994 ENST00000649159.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.292
• Publications: 0 publications found

Genes affected

ENSG00000265994 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.547 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000649159.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000265994	ENST00000649159.1		n.217-15114A>G		intron	N/A
	ENSG00000265994	ENST00000812054.1		n.729-28599A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.415 AC: 62956 AN: 151714 Hom.: 15456 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.608

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.651

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.415 AC: 62970 AN: 151832 Hom.: 15457 Cov.: 32 AF XY: 0.411 AC XY: 30495 AN XY: 74184

African (AFR) AF: 0.153 AC: 6359 AN: 41436

American (AMR) AF: 0.431 AC: 6556 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.651 AC: 2253 AN: 3460

East Asian (EAS) AF: 0.263 AC: 1347 AN: 5126

South Asian (SAS) AF: 0.421 AC: 2024 AN: 4812

European-Finnish (FIN) AF: 0.497 AC: 5235 AN: 10532

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.552 AC: 37466 AN: 67930

Other (OTH) AF: 0.482 AC: 1016 AN: 2106

Alfa AF: 0.520 Hom.: 35889

Bravo AF: 0.403

Asia WGS AF: 0.368 AC: 1282 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.42
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs11083301; hg19: chr18-26353724;