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GeneBe

rs12225197

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The XR_007062619.1(LOC102723370):​n.649+3956G>A 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 0.0223 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

LOC102723370
XR_007062619.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.491
Variant links:
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]

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ACMG classification

Classification made for transcript

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 UniProt
LOC102723370XR_007062619.1 linkuse as main transcriptn.649+3956G>A intron_variant, non_coding_transcript_variant
LOC102723370XR_007062621.1 linkuse as main transcriptn.199+3956G>A intron_variant, non_coding_transcript_variant
LOC102723370XR_931109.3 linkuse as main transcriptn.200-1901G>A intron_variant, non_coding_transcript_variant
LOC102723370XR_931110.3 linkuse as main transcriptn.199+3956G>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ANO5ENST00000664026.1 linkuse as main transcriptn.68+16134G>A intron_variant, non_coding_transcript_variant
ANO5ENST00000682428.1 linkuse as main transcriptn.196+3956G>A intron_variant, non_coding_transcript_variant
ANO5ENST00000683812.1 linkuse as main transcriptn.187-1901G>A intron_variant, non_coding_transcript_variant

Frequencies

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs12225197; hg19: chr11-21820406; API