9-123266116-C-G

Position:

• chr9-123266116-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018387.5(STRBP):​c.-302+2320G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.773 in 152,080 control chromosomes in the GnomAD database, including 46,684 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 0.77 (46684 hom., cov: 31)
• Consequence: STRBP NM_018387.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0790

Genes affected

STRBP (HGNC:16462): (spermatid perinuclear RNA binding protein) Enables RNA binding activity. Predicted to be involved in spermatogenesis. Predicted to act upstream of or within mechanosensory behavior and spermatid development. Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

STRBP (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.961 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STRBP	NM_018387.5	c.-302+2320G>C		intron_variant		ENST00000348403.10	NP_060857.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STRBP	ENST00000348403.10	c.-302+2320G>C		intron_variant		1	NM_018387.5	ENSP00000321347.7
STRBP	ENST00000360998.3	c.-315+2320G>C		intron_variant		1		ENSP00000354271.3
STRBP	ENST00000407982.6	n.-165+2320G>C		intron_variant		1		ENSP00000384292.2

Frequencies

GnomAD3 genomes AF: 0.773 AC: 117448 AN: 151962 Hom.: 46615 Cov.: 31

Gnomad AFR AF: 0.941

Gnomad AMI AF: 0.609

Gnomad AMR AF: 0.811

Gnomad ASJ AF: 0.726

Gnomad EAS AF: 0.984

Gnomad SAS AF: 0.734

Gnomad FIN AF: 0.746

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.659

Gnomad OTH AF: 0.753

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

GnomAD4 genome AF: 0.773 AC: 117580 AN: 152080 Hom.: 46684 Cov.: 31 AF XY: 0.778 AC XY: 57808 AN XY: 74324

Gnomad4 AFR AF: 0.941

Gnomad4 AMR AF: 0.811

Gnomad4 ASJ AF: 0.726

Gnomad4 EAS AF: 0.984

Gnomad4 SAS AF: 0.734

Gnomad4 FIN AF: 0.746

Gnomad4 NFE AF: 0.659

Gnomad4 OTH AF: 0.756

Alfa AF: 0.714 Hom.: 4656

Bravo AF: 0.787

Asia WGS AF: 0.884 AC: 3074 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.7
DANN	Benign	0.66

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: rs7863265; hg19: chr9-126028395; COSMIC: COSV62116771;