rs11026412

Positions:

• chr11-22092547-G-A

Variant summary

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

The ENST00000659342.1(ENSG00000287962):​n.487-1117C>T 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 0.179 in 151,832 control chromosomes in the GnomAD database, including 2,669 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 0.18 (2669 hom., cov: 32)
• Consequence: ENST00000659342.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252

Genes affected

(HGNC:):

ANO5 (HGNC:27337): (anoctamin 5) This gene encodes a member of the anoctamin family of transmembrane proteins. The encoded protein is likely a calcium activated chloride channel. Mutations in this gene have been associated with gnathodiaphyseal dysplasia. Alternatively spliced transcript variants have been described. [provided by RefSeq, Nov 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.353 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC102723370	XR_007062619.1	n.924+12845G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000659342.1	n.487-1117C>T		intron_variant, non_coding_transcript_variant
ANO5	ENST00000648804.1	n.544+12845G>A		intron_variant, non_coding_transcript_variant
ANO5	ENST00000682428.1	n.964+12845G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27207 AN: 151712 Hom.: 2668 Cov.: 32

Gnomad AFR AF: 0.0991

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.179 AC: 27213 AN: 151832 Hom.: 2669 Cov.: 32 AF XY: 0.182 AC XY: 13487 AN XY: 74176

Gnomad4 AFR AF: 0.0990

Gnomad4 AMR AF: 0.202

Gnomad4 ASJ AF: 0.243

Gnomad4 EAS AF: 0.366

Gnomad4 SAS AF: 0.241

Gnomad4 FIN AF: 0.192

Gnomad4 NFE AF: 0.199

Gnomad4 OTH AF: 0.199

Alfa AF: 0.202 Hom.: 3419

Bravo AF: 0.178

Asia WGS AF: 0.237 AC: 822 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.4
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11026412; hg19: chr11-22114093; COSMIC: COSV56522946;