rs324205

Positions:

• chr11-21980439-C-G

Variant summary

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

The ENST00000648804.1(ANO5):​n.270-2527C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 152,126 control chromosomes in the GnomAD database, including 3,979 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 0.21 (3979 hom., cov: 32)
• Consequence: ANO5 ENST00000648804.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.297

Genes affected

ANO5 (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 (EAS) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC102723370	XR_007062617.1	n.313-2527C>G		intron_variant
LOC102723370	XR_007062618.1	n.114-2527C>G		intron_variant
LOC102723370	XR_007062619.1	n.650-2527C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANO5	ENST00000648804.1	n.270-2527C>G		intron_variant
ANO5	ENST00000682428.1	n.802+35528C>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32333 AN: 152008 Hom.: 3976 Cov.: 32

Gnomad AFR AF: 0.0996

Gnomad AMI AF: 0.380

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.213 AC: 32349 AN: 152126 Hom.: 3979 Cov.: 32 AF XY: 0.211 AC XY: 15717 AN XY: 74360

Gnomad4 AFR AF: 0.0995

Gnomad4 AMR AF: 0.236

Gnomad4 ASJ AF: 0.254

Gnomad4 EAS AF: 0.453

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.207

Gnomad4 NFE AF: 0.252

Gnomad4 OTH AF: 0.253

Alfa AF: 0.220 Hom.: 492

Bravo AF: 0.215

Asia WGS AF: 0.286 AC: 993 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	1.4
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs324205; hg19: chr11-22001985;