rs7998202

chr13-112677554-A-G

Variant summary

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

The NR_164109.1(ATP11AUN):n.556-1623A>G variant causes a intron, non coding transcript change. The variant allele was found at a frequency of 0.17 in 152,030 control chromosomes in the GnomAD database, including 2,571 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 0.17 (2571 hom., cov: 33)
• Consequence: ATP11AUN NR_164109.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned

Genes affected

ATP11AUN (HGNC:33793): (ATP11A upstream neighbor lncRNA)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.258 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATP11AUN	NR_164109.1	n.556-1623A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATP11AUN	ENST00000623100.2	n.556-1623A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25811 AN: 151910 Hom.: 2572 Cov.: 33

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.0681

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.170 AC: 25830 AN: 152030 Hom.: 2571 Cov.: 33 AF XY: 0.168 AC XY: 12498 AN XY: 74324

Gnomad4 AFR AF: 0.262

Gnomad4 AMR AF: 0.179

Gnomad4 ASJ AF: 0.127

Gnomad4 EAS AF: 0.0682

Gnomad4 SAS AF: 0.100

Gnomad4 FIN AF: 0.129

Gnomad4 NFE AF: 0.134

Gnomad4 OTH AF: 0.159

Alfa AF: 0.138 Hom.: 1707

Bravo AF: 0.179

Asia WGS AF: 0.101 AC: 350 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	3.0
Dann	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7998202; hg19: chr13-113331868;