rs11083301

Positions:

• chr18-28773760-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000649159.1(ENSG00000265994):​n.217-15114A>G variant causes a intron, non coding transcript 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: ENST00000649159.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.292

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000649159.1	n.217-15114A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.153

Gnomad4 AMR AF: 0.431

Gnomad4 ASJ AF: 0.651

Gnomad4 EAS AF: 0.263

Gnomad4 SAS AF: 0.421

Gnomad4 FIN AF: 0.497

Gnomad4 NFE AF: 0.552

Gnomad4 OTH AF: 0.482

Alfa AF: 0.534 Hom.: 29251

Bravo AF: 0.403

Asia WGS AF: 0.368 AC: 1282 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11083301; hg19: chr18-26353724;