rs11080384

chr18-10088965-A-G

Variant summary

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

The ENST00000685786.1(ENSG00000265554):n.388+2740A>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 0.241 in 152,140 control chromosomes in the GnomAD database, including 4,684 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 0.24 (4684 hom., cov: 33)
• Consequence: ENST00000685786.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105371984	XR_935136.3	n.665+2740A>G		intron_variant, non_coding_transcript_variant
LOC105371984	XR_935137.3	n.665+2740A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000685786.1	n.388+2740A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.241 AC: 36579 AN: 152022 Hom.: 4685 Cov.: 33

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.403

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.241 AC: 36593 AN: 152140 Hom.: 4684 Cov.: 33 AF XY: 0.237 AC XY: 17660 AN XY: 74370

Gnomad4 AFR AF: 0.155

Gnomad4 AMR AF: 0.216

Gnomad4 ASJ AF: 0.311

Gnomad4 EAS AF: 0.209

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.262

Gnomad4 NFE AF: 0.294

Gnomad4 OTH AF: 0.248

Alfa AF: 0.263 Hom.: 681

Bravo AF: 0.235

Asia WGS AF: 0.202 AC: 702 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.21
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11080384; hg19: chr18-10088962;