Variant 11-429659-C-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001012302.3(ANO9):c.833-7G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.585 in 1,612,230 control chromosomes in the GnomAD database, including 278,566 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.58 ( 25442 hom., cov: 33)

Exomes 𝑓: 0.59 ( 253124 hom. )

Consequence

ANO9
NM_001012302.3 splice_region, intron

Scores

Splicing: ADA: 0.00008639

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.20

Variant links:

Genes affected

ANO9 (HGNC:20679): (anoctamin 9) The protein encoded by this gene is a member of the TMEM16 (anoctamin) family of proteins, some of which form integral membrane calcium-activated chloride channels. The function of the encoded protein has yet to be elucidated, although it may have channel-forming abilities and also may have phospholipid scramblase activity. This gene has been observed to be upregulated in stage II and III colorectal cancers. [provided by RefSeq, Dec 2016]

ANO9 links:

ANO9 (HGNC:):

ANO9 links:

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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=-0.85).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.598 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANO9	NM_001012302.3 linkuse as main transcript	c.833-7G>A		splice_region_variant, intron_variant		ENST00000332826.7	NP_001012302.2	A1A5B4-1
ANO9	NM_001347882.2 linkuse as main transcript	c.401-7G>A		splice_region_variant, intron_variant			NP_001334811.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANO9	ENST00000332826.7 linkuse as main transcript	c.833-7G>A		splice_region_variant, intron_variant		1	NM_001012302.3	ENSP00000332788.6		A1A5B4-1

Frequencies

GnomAD3 genomes

AF:

0.576

AC:

87516

AN:

151938

Hom.:

25415

Cov.:

show subpopulations

Gnomad AFR

AF:

0.569

Gnomad AMI

AF:

0.546

Gnomad AMR

AF:

0.553

Gnomad ASJ

AF:

0.595

Gnomad EAS

AF:

0.373

Gnomad SAS

AF:

0.558

Gnomad FIN

AF:

0.565

Gnomad MID

AF:

0.674

Gnomad NFE

AF:

0.603

Gnomad OTH

AF:

0.582

GnomAD3 exomes

AF:

0.558

AC:

138644

AN:

248374

Hom.:

39279

AF XY:

0.563

AC XY:

75998

AN XY:

135044

show subpopulations

Gnomad AFR exome

AF:

0.567

Gnomad AMR exome

AF:

0.496

Gnomad ASJ exome

AF:

0.583

Gnomad EAS exome

AF:

0.366

Gnomad SAS exome

AF:

0.565

Gnomad FIN exome

AF:

0.561

Gnomad NFE exome

AF:

0.601

Gnomad OTH exome

AF:

0.590

GnomAD4 exome

AF:

0.586

AC:

856348

AN:

1460174

Hom.:

253124

Cov.:

AF XY:

0.586

AC XY:

425885

AN XY:

726394

show subpopulations

Gnomad4 AFR exome

AF:

0.563

Gnomad4 AMR exome

AF:

0.503

Gnomad4 ASJ exome

AF:

0.589

Gnomad4 EAS exome

AF:

0.349

Gnomad4 SAS exome

AF:

0.576

Gnomad4 FIN exome

AF:

0.565

Gnomad4 NFE exome

AF:

0.600

Gnomad4 OTH exome

AF:

0.588

GnomAD4 genome

AF:

0.576

AC:

87581

AN:

152056

Hom.:

25442

Cov.:

AF XY:

0.573

AC XY:

42609

AN XY:

74330

show subpopulations

Gnomad4 AFR

AF:

0.569

Gnomad4 AMR

AF:

0.552

Gnomad4 ASJ

AF:

0.595

Gnomad4 EAS

AF:

0.373

Gnomad4 SAS

AF:

0.559

Gnomad4 FIN

AF:

0.565

Gnomad4 NFE

AF:

0.603

Gnomad4 OTH

AF:

0.585

Alfa

AF:

0.595

Hom.:

46798

Bravo

AF:

0.571

Asia WGS

AF:

0.480

AC:

1671

AN:

3478

EpiCase

AF:

0.605

EpiControl

AF:

0.614

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.60

DANN

Benign

0.52

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000086

dbscSNV1_RF

Benign

0.0

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over