dbSNP rs1200814: ANKRD30A:n.7524-1636A>G (chr10-37246482-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The XR_007062015.1(ANKRD30A):n.7524-1636A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.803 in 152,188 control chromosomes in the GnomAD database, including 49,455 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 0.80 ( 49455 hom., cov: 33)

Consequence

ANKRD30A
XR_007062015.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.506

Publications

0 publications found

Variant links:

Genes affected

ANKRD30A (HGNC:17234): (ankyrin repeat domain 30A) This gene encodes a DNA-binding transcription factor that is uniquely expressed in mammary epithelium and the testis. Altered expression levels have been associated with breast cancer progression. [provided by RefSeq, Nov 2016]

ANKRD30A links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.863 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKRD30A	XR_007062015.1 link	n.7524-1636A>G		intron_variant	Intron 48 of 54
ANKRD30A	XR_930524.4 link	n.*5A>G		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.803

AC:

122119

AN:

152070

Hom.:

49456

Cov.:

show subpopulations

Gnomad AFR

AF:

0.687

Gnomad AMI

AF:

0.791

Gnomad AMR

AF:

0.876

Gnomad ASJ

AF:

0.876

Gnomad EAS

AF:

0.869

Gnomad SAS

AF:

0.857

Gnomad FIN

AF:

0.890

Gnomad MID

AF:

0.807

Gnomad NFE

AF:

0.831

Gnomad OTH

AF:

0.820

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

GnomAD4 genome

AF:

0.803

AC:

122148

AN:

152188

Hom.:

49455

Cov.:

AF XY:

0.807

AC XY:

60013

AN XY:

74400

show subpopulations

African (AFR)

AF:

0.686

AC:

28454

AN:

41490

American (AMR)

AF:

0.876

AC:

13391

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.876

AC:

3038

AN:

3470

East Asian (EAS)

AF:

0.868

AC:

4495

AN:

5176

South Asian (SAS)

AF:

0.857

AC:

4138

AN:

4828

European-Finnish (FIN)

AF:

0.890

AC:

9427

AN:

10594

Middle Eastern (MID)

AF:

0.813

AC:

239

AN:

294

European-Non Finnish (NFE)

AF:

0.831

AC:

56512

AN:

68020

Other (OTH)

AF:

0.820

AC:

1733

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1211

2423

3634

4846

6057

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.828

Hom.:

36844

Bravo

AF:

0.796

Asia WGS

AF:

0.844

AC:

2932

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

4.9

(source)

DANN

Benign

0.63

PhyloP100

0.51

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

Publications

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rs1200814

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over