rs7998202

Variant names:

• chr13-112677554-A-G
• rs7998202
• ENST00000623100.2:n.556-1623A>G

Variant summary

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

The ENST00000623100.2(ATP11AUN):​n.556-1623A>G variant causes a intron 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 ENST00000623100.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned
• Publications: 30 publications found

Genes affected

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

ENSG00000309697 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000623100.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATP11AUN	NR_164109.1		n.556-1623A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATP11AUN	ENST00000623100.2	TSL:2	n.556-1623A>G		intron	N/A
	ENSG00000309697	ENST00000843113.1		n.314+993T>C		intron	N/A

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

African (AFR) AF: 0.262 AC: 10854 AN: 41420

American (AMR) AF: 0.179 AC: 2738 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 439 AN: 3468

East Asian (EAS) AF: 0.0682 AC: 354 AN: 5188

South Asian (SAS) AF: 0.100 AC: 482 AN: 4814

European-Finnish (FIN) AF: 0.129 AC: 1361 AN: 10582

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.134 AC: 9090 AN: 67976

Other (OTH) AF: 0.159 AC: 336 AN: 2108

Alfa AF: 0.147 Hom.: 5413

Bravo AF: 0.179

Asia WGS AF: 0.101 AC: 350 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.0
DANN	Benign	0.37
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: rs7998202; hg19: chr13-113331868;