rs7120076

Variant names:

• chr11-111533959-A-G
• rs7120076
• NM_001100388.2:c.399+154A>G

Variant summary

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

The NM_001100388.2(HOATZ):​c.399+154A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0363 in 152,322 control chromosomes in the GnomAD database, including 345 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 0.036 (345 hom., cov: 33)
• Consequence: HOATZ NM_001100388.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.592
• Publications: 1 publications found

Genes affected

HOATZ (HGNC:25061): (HOATZ cilia and flagella associated protein) Predicted to be involved in axoneme assembly; flagellated sperm motility; and spermatogenesis. Predicted to be located in cilium and cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HOATZ	NM_001100388.2	c.399+154A>G		intron_variant	Intron 4 of 5	ENST00000375618.9	NP_001093858.1
HOATZ	NM_207430.2	c.480+154A>G		intron_variant	Intron 5 of 6		NP_997313.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HOATZ	ENST00000375618.9	c.399+154A>G		intron_variant	Intron 4 of 5	1	NM_001100388.2	ENSP00000364768.4
HOATZ	ENST00000332814.6	c.480+154A>G		intron_variant	Intron 5 of 6	5		ENSP00000333845.6
HOATZ	ENST00000529167.5	c.480+154A>G		intron_variant	Intron 5 of 5	2		ENSP00000432911.1
HOATZ	ENST00000529661.1	n.*219+154A>G		intron_variant	Intron 3 of 4	3		ENSP00000435029.1

Frequencies

GnomAD3 genomes AF: 0.0362 AC: 5513 AN: 152204 Hom.: 343 Cov.: 33

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0136

Gnomad ASJ AF: 0.00577

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000827

Gnomad FIN AF: 0.0000941

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.000882

Gnomad OTH AF: 0.0282

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

GnomAD4 genome AF: 0.0363 AC: 5530 AN: 152322 Hom.: 345 Cov.: 33 AF XY: 0.0357 AC XY: 2662 AN XY: 74494

African (AFR) AF: 0.125 AC: 5174 AN: 41550

American (AMR) AF: 0.0136 AC: 208 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.00577 AC: 20 AN: 3466

East Asian (EAS) AF: 0.00 AC: 0 AN: 5196

South Asian (SAS) AF: 0.000621 AC: 3 AN: 4830

European-Finnish (FIN) AF: 0.0000941 AC: 1 AN: 10622

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.000882 AC: 60 AN: 68032

Other (OTH) AF: 0.0279 AC: 59 AN: 2116

Alfa AF: 0.0190 Hom.: 91

Bravo AF: 0.0413

Asia WGS AF: 0.00953 AC: 33 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.5
DANN	Benign	0.79
PhyloP100		0.59
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs7120076; hg19: chr11-111404684;