XR_007062015.1:n.7524-1636A>G

Variant names:

• chr10-37246482-A-G
• rs1200814
• XR_007062015.1:n.7524-1636A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.506
• Publications: 0 publications found

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]

ACMG classification

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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.803 AC: 122119 AN: 152070 Hom.: 49456 Cov.: 33

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.: 33 AF XY: 0.807 AC XY: 60013 AN XY: 74400

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

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.9
DANN	Benign	0.63
PhyloP100		0.51
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1200814; hg19: chr10-37535410;