rs7328960

Variant names:

• chr13-112674402-C-T
• rs7328960
• ENST00000623100.2:n.556-4775C>T

Variant summary

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

The ENST00000623100.2(ATP11AUN):​n.556-4775C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.529 in 152,060 control chromosomes in the GnomAD database, including 21,789 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 0.53 (21789 hom., cov: 33)
• Consequence: ATP11AUN ENST00000623100.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47
• Publications: 4 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.636 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATP11AUN	NR_164109.1	n.556-4775C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATP11AUN	ENST00000623100.2	n.556-4775C>T		intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes AF: 0.529 AC: 80409 AN: 151942 Hom.: 21770 Cov.: 33

Gnomad AFR AF: 0.642

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.541

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.527

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

GnomAD4 genome AF: 0.529 AC: 80474 AN: 152060 Hom.: 21789 Cov.: 33 AF XY: 0.530 AC XY: 39367 AN XY: 74310

African (AFR) AF: 0.642 AC: 26655 AN: 41508

American (AMR) AF: 0.438 AC: 6683 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.518 AC: 1797 AN: 3466

East Asian (EAS) AF: 0.541 AC: 2804 AN: 5184

South Asian (SAS) AF: 0.520 AC: 2502 AN: 4816

European-Finnish (FIN) AF: 0.492 AC: 5183 AN: 10544

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.488 AC: 33150 AN: 67958

Other (OTH) AF: 0.528 AC: 1114 AN: 2108

Alfa AF: 0.499 Hom.: 32034

Bravo AF: 0.529

Asia WGS AF: 0.518 AC: 1801 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.28
DANN	Benign	0.81
PhyloP100		-1.5
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: rs7328960; hg19: chr13-113328716;