chr9-4636900-T-C

Variant names:

• chr9-4636900-T-C
• rs4740796
• NM_001353486.2:c.227-1501A>G

Variant summary

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

The NM_001353486.2(SPATA6L):​c.227-1501A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 152,184 control chromosomes in the GnomAD database, including 1,463 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 0.12 (1463 hom., cov: 32)
• Consequence: SPATA6L NM_001353486.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.40
• Publications: 1 publications found

Genes affected

SPATA6L (HGNC:25472): (spermatogenesis associated 6 like) Predicted to enable myosin light chain binding activity. Predicted to be involved in spermatogenesis. Predicted to be located in sperm connecting piece. [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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.322 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPATA6L	NM_001353486.2	c.227-1501A>G		intron_variant	Intron 3 of 11	ENST00000682582.1	NP_001340415.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPATA6L	ENST00000682582.1	c.227-1501A>G		intron_variant	Intron 3 of 11		NM_001353486.2	ENSP00000506787.1

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17573 AN: 152066 Hom.: 1461 Cov.: 32

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.0548

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0685

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0549

Gnomad OTH AF: 0.0920

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

GnomAD4 genome AF: 0.116 AC: 17605 AN: 152184 Hom.: 1463 Cov.: 32 AF XY: 0.117 AC XY: 8720 AN XY: 74406

African (AFR) AF: 0.202 AC: 8391 AN: 41500

American (AMR) AF: 0.132 AC: 2019 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0548 AC: 190 AN: 3468

East Asian (EAS) AF: 0.335 AC: 1731 AN: 5172

South Asian (SAS) AF: 0.113 AC: 546 AN: 4828

European-Finnish (FIN) AF: 0.0685 AC: 726 AN: 10606

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0549 AC: 3732 AN: 68002

Other (OTH) AF: 0.0963 AC: 203 AN: 2108

Alfa AF: 0.0548 Hom.: 107

Bravo AF: 0.126

Asia WGS AF: 0.244 AC: 845 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.0
DANN	Benign	0.79
PhyloP100		-2.4
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: rs4740796; hg19: chr9-4636900;