chr5-95695580-A-G

Variant names:

• chr5-95695580-A-G
• rs212998
• NM_001349303.2:c.-24+3008T>C

Variant summary

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

The NM_001349303.2(SPATA9):​c.-24+3008T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.569 in 152,070 control chromosomes in the GnomAD database, including 24,767 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 0.57 (24767 hom., cov: 33)
• Consequence: SPATA9 NM_001349303.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.840
• Publications: 1 publications found

Genes affected

SPATA9 (HGNC:22988): (spermatogenesis associated 9) Predicted to be involved in cell differentiation and spermatogenesis. Predicted to be integral component of membrane. [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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.779 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001349303.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPATA9	NM_001349303.2		c.-24+3008T>C		intron	N/A	NP_001336232.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPATA9	ENST00000379990.9	TSL:3	n.124+3008T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.568 AC: 86383 AN: 151952 Hom.: 24735 Cov.: 33

Gnomad AFR AF: 0.590

Gnomad AMI AF: 0.590

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.797

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.643

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.541

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.569 AC: 86465 AN: 152070 Hom.: 24767 Cov.: 33 AF XY: 0.574 AC XY: 42683 AN XY: 74338

African (AFR) AF: 0.589 AC: 24417 AN: 41448

American (AMR) AF: 0.525 AC: 8017 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.452 AC: 1566 AN: 3468

East Asian (EAS) AF: 0.799 AC: 4138 AN: 5180

South Asian (SAS) AF: 0.605 AC: 2915 AN: 4818

European-Finnish (FIN) AF: 0.643 AC: 6812 AN: 10588

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.541 AC: 36757 AN: 67972

Other (OTH) AF: 0.556 AC: 1176 AN: 2116

Alfa AF: 0.559 Hom.: 3133

Bravo AF: 0.563

Asia WGS AF: 0.665 AC: 2312 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.0
DANN	Benign	0.51
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs212998; hg19: chr5-95031284;