rs1200814

chr10-37246482-A-G

Variant summary

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

The XR_007062015.1(ANKRD30A):n.7524-1636A>G 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 0.803 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.506

Genes affected

ANKRD30A (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
ANKRD30A	XR_007062015.1	n.7524-1636A>G		intron_variant, non_coding_transcript_variant
ANKRD30A	XR_930524.4			downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.686

Gnomad4 AMR AF: 0.876

Gnomad4 ASJ AF: 0.876

Gnomad4 EAS AF: 0.868

Gnomad4 SAS AF: 0.857

Gnomad4 FIN AF: 0.890

Gnomad4 NFE AF: 0.831

Gnomad4 OTH AF: 0.820

Alfa AF: 0.828 Hom.: 26691

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
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1200814; hg19: chr10-37535410;