rs12295951

chr11-21949003-C-T

Variant summary

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

The XR_007062619.1(LOC102723370):n.650-33963C>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 0.172 in 152,044 control chromosomes in the GnomAD database, including 2,313 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 (2313 hom., cov: 32)
• Consequence: LOC102723370 XR_007062619.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.390

Genes affected

LOC102723370 (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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102723370	XR_007062619.1	n.650-33963C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANO5	ENST00000648804.1	n.270-33963C>T		intron_variant, non_coding_transcript_variant
ANO5	ENST00000682428.1	n.802+4092C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26102 AN: 151926 Hom.: 2314 Cov.: 32

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.0229

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.172 AC: 26114 AN: 152044 Hom.: 2313 Cov.: 32 AF XY: 0.173 AC XY: 12840 AN XY: 74302

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.119

Gnomad4 ASJ AF: 0.205

Gnomad4 EAS AF: 0.0228

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.226

Gnomad4 NFE AF: 0.174

Gnomad4 OTH AF: 0.173

Alfa AF: 0.172 Hom.: 1463

Bravo AF: 0.163

Asia WGS AF: 0.0750 AC: 263 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	4.7
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12295951; hg19: chr11-21970549;