chr11-21798860-G-A

Position:

• chr11-21798860-G-A

Variant summary

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

The ENST00000664026.1(ANO5):​n.68+16134G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0223 in 151,962 control chromosomes in the GnomAD database, including 227 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 0.022 (227 hom., cov: 32)
• Consequence: ANO5 ENST00000664026.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.491

Genes affected

ANO5 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC102723370	XR_007062619.1	n.649+3956G>A		intron_variant
LOC102723370	XR_007062621.1	n.199+3956G>A		intron_variant
LOC102723370	XR_931109.3	n.200-1901G>A		intron_variant
LOC102723370	XR_931110.3	n.199+3956G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANO5	ENST00000664026.1	n.68+16134G>A		intron_variant
ANO5	ENST00000682428.1	n.196+3956G>A		intron_variant
ANO5	ENST00000683812.1	n.187-1901G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0224 AC: 3394 AN: 151844 Hom.: 228 Cov.: 32

Gnomad AFR AF: 0.00331

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0988

Gnomad ASJ AF: 0.00116

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.0957

Gnomad FIN AF: 0.0126

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00159

Gnomad OTH AF: 0.0215

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

GnomAD4 genome AF: 0.0223 AC: 3390 AN: 151962 Hom.: 227 Cov.: 32 AF XY: 0.0265 AC XY: 1972 AN XY: 74298

Gnomad4 AFR AF: 0.00332

Gnomad4 AMR AF: 0.0989

Gnomad4 ASJ AF: 0.00116

Gnomad4 EAS AF: 0.194

Gnomad4 SAS AF: 0.0946

Gnomad4 FIN AF: 0.0126

Gnomad4 NFE AF: 0.00159

Gnomad4 OTH AF: 0.0213

Alfa AF: 0.00727 Hom.: 112

Bravo AF: 0.0294

Asia WGS AF: 0.119 AC: 414 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.9
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12225197; hg19: chr11-21820406;