7-135249016-C-A

Variant names:

• chr7-135249016-C-A
• rs2033050
• NM_001394401.1:c.879+2314C>A

Variant summary

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

The NM_001394401.1(STRA8):​c.879+2314C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 152,068 control chromosomes in the GnomAD database, including 5,582 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 0.25 (5582 hom., cov: 32)
• Consequence: STRA8 NM_001394401.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171
• Publications: 3 publications found

Genes affected

STRA8 (HGNC:30653): (stimulated by retinoic acid 8) This gene encodes a retinoic acid-responsive protein. A homologous protein in mouse has been shown to be involved in the regulation of meiotic initiation in both spermatogenesis and oogenesis, though feature differences between the mouse and human proteins suggest that these homologs are not entirely functionally equivalent. It is thought that this gene may play a role in spermatogenesis in humans. [provided by RefSeq, Nov 2010]

STRA8 Gene-Disease associations (from GenCC):

• male infertility with azoospermia or oligozoospermia due to single gene mutation

  Inheritance: AR Classification: MODERATE Submitted by: King Faisal Specialist Hospital and Research Center

ENSG00000290805 (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 (EAS) allele frequency at 95% confidence interval = 0.547 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STRA8	NM_001394401.1	c.879+2314C>A		intron_variant	Intron 6 of 8	ENST00000662584.2	NP_001381330.1
STRA8	NM_182489.3	c.666+2314C>A		intron_variant	Intron 6 of 8		NP_872295.2
STRA8	XM_011516137.3	c.879+2314C>A		intron_variant	Intron 5 of 7		XP_011514439.1
STRA8	XM_047420324.1	c.879+2314C>A		intron_variant	Intron 6 of 8		XP_047276280.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STRA8	ENST00000662584.2	c.879+2314C>A		intron_variant	Intron 6 of 8		NM_001394401.1	ENSP00000499386.1
STRA8	ENST00000275764.3	c.732+2314C>A		intron_variant	Intron 6 of 8	1		ENSP00000275764.3
STRA8	ENST00000667288.1	c.666+2314C>A		intron_variant	Intron 6 of 8			ENSP00000499721.1
ENSG00000290805	ENST00000637483.1	n.404-1799G>T		intron_variant	Intron 3 of 4	5

Frequencies

GnomAD3 genomes AF: 0.246 AC: 37415 AN: 151950 Hom.: 5585 Cov.: 32

Gnomad AFR AF: 0.0875

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.564

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.246 AC: 37408 AN: 152068 Hom.: 5582 Cov.: 32 AF XY: 0.249 AC XY: 18515 AN XY: 74292

African (AFR) AF: 0.0872 AC: 3622 AN: 41516

American (AMR) AF: 0.299 AC: 4570 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 609 AN: 3470

East Asian (EAS) AF: 0.564 AC: 2906 AN: 5156

South Asian (SAS) AF: 0.242 AC: 1162 AN: 4810

European-Finnish (FIN) AF: 0.312 AC: 3291 AN: 10548

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.300 AC: 20371 AN: 67970

Other (OTH) AF: 0.258 AC: 546 AN: 2114

Alfa AF: 0.281 Hom.: 13372

Bravo AF: 0.240

Asia WGS AF: 0.378 AC: 1312 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	0.94
DANN	Benign	0.80
PhyloP100		0.17
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: rs2033050; hg19: chr7-134933768;