rs2033050

Positions:

• chr7-135249016-C-A
• chr7-135249016-C-G
• chr7-135249016-C-T

Variant summary

Our verdict is Benign. Variant got -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

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]

ENSG00000290805 (HGNC:):

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STRA8	NM_001394401.1	c.879+2314C>A		intron_variant		ENST00000662584.2	NP_001381330.1
STRA8	NM_182489.3	c.666+2314C>A		intron_variant			NP_872295.2
STRA8	XM_011516137.3	c.879+2314C>A		intron_variant			XP_011514439.1
STRA8	XM_047420324.1	c.879+2314C>A		intron_variant			XP_047276280.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STRA8	ENST00000662584.2	c.879+2314C>A		intron_variant			NM_001394401.1	ENSP00000499386.1
STRA8	ENST00000275764.3	c.732+2314C>A		intron_variant		1		ENSP00000275764.3
STRA8	ENST00000667288.1	c.666+2314C>A		intron_variant				ENSP00000499721.1
ENSG00000290805	ENST00000637483.1	n.404-1799G>T		intron_variant		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

Gnomad4 AFR AF: 0.0872

Gnomad4 AMR AF: 0.299

Gnomad4 ASJ AF: 0.176

Gnomad4 EAS AF: 0.564

Gnomad4 SAS AF: 0.242

Gnomad4 FIN AF: 0.312

Gnomad4 NFE AF: 0.300

Gnomad4 OTH AF: 0.258

Alfa AF: 0.285 Hom.: 3206

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs2033050; hg19: chr7-134933768;