NM_213599.3:c.-156_-155insAGGGGAATGAGGAGGAAGAGGAGG

Variant names:

• chr11-22193331-A-AAGGAGGAGGGGAATGAGGAGGAAG
• rs71034576
• NM_213599.3:c.-156_-155insAGGGGAATGAGGAGGAAGAGGAGG

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

The NM_213599.3(ANO5):​c.-156_-155insAGGGGAATGAGGAGGAAGAGGAGG variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0024 (1 hom., cov: 0)
  • Exomes 𝑓: 0.00022 (3 hom.)
  • Failed GnomAD Quality Control
• Consequence: ANO5 NM_213599.3 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.16

Genes affected

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 -8 ACMG points.

• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00243 (367/150742) while in subpopulation AFR AF= 0.00874 (359/41078). AF 95% confidence interval is 0.00799. There are 1 homozygotes in gnomad4. There are 162 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
• BS2: High AC in GnomAd4 at 367 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANO5	NM_213599.3	c.-156_-155insAGGGGAATGAGGAGGAAGAGGAGG		5_prime_UTR_variant	Exon 1 of 22	ENST00000324559.9	NP_998764.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANO5	ENST00000324559	c.-156_-155insAGGGGAATGAGGAGGAAGAGGAGG		5_prime_UTR_variant	Exon 1 of 22	1	NM_213599.3	ENSP00000315371.9

Frequencies

GnomAD3 genomes AF: 0.00243 AC: 366 AN: 150624 Hom.: 1 Cov.: 0

Gnomad AFR AF: 0.00874

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000198

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00637

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00145

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000223 AC: 286 AN: 1279960 Hom.: 3 Cov.: 57 AF XY: 0.000208 AC XY: 129 AN XY: 620608

Gnomad4 AFR exome AF: 0.00917

Gnomad4 AMR exome AF: 0.000281

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000313

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000295

Gnomad4 OTH exome AF: 0.000284

GnomAD4 genome AF: 0.00243 AC: 367 AN: 150742 Hom.: 1 Cov.: 0 AF XY: 0.00220 AC XY: 162 AN XY: 73576

Gnomad4 AFR AF: 0.00874

Gnomad4 AMR AF: 0.000197

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00144

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs71034576; hg19: chr11-22214877;