rs16921669

Variant names:

• chr9-4635232-G-A
• rs16921669
• NM_001353486.2:c.351+43C>T

Your query was ambiguous. Multiple possible variants found:

• chr9-4635232-G-A
• chr9-4635232-G-C

Variant summary

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

The NM_001353486.2(SPATA6L):​c.351+43C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.077 in 1,469,260 control chromosomes in the GnomAD database, including 8,194 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 0.14 (2189 hom., cov: 32)
  • Exomes 𝑓: 0.070 (6005 hom.)
• Consequence: SPATA6L NM_001353486.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.757
• Publications: 8 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.32 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPATA6L	NM_001353486.2	c.351+43C>T		intron_variant	Intron 4 of 11	ENST00000682582.1	NP_001340415.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPATA6L	ENST00000682582.1	c.351+43C>T		intron_variant	Intron 4 of 11		NM_001353486.2	ENSP00000506787.1

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20618 AN: 151886 Hom.: 2176 Cov.: 32

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.0548

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.0686

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0550

Gnomad OTH AF: 0.101

GnomAD2 exomes AF: 0.102 AC: 14097 AN: 137746 AF XY: 0.0942

Gnomad AFR exome AF: 0.281

Gnomad AMR exome AF: 0.158

Gnomad ASJ exome AF: 0.0529

Gnomad EAS exome AF: 0.332

Gnomad FIN exome AF: 0.0678

Gnomad NFE exome AF: 0.0560

Gnomad OTH exome AF: 0.0846

GnomAD4 exome AF: 0.0702 AC: 92445 AN: 1317256 Hom.: 6005 Cov.: 30 AF XY: 0.0694 AC XY: 44845 AN XY: 646142

African (AFR) AF: 0.284 AC: 7399 AN: 26086

American (AMR) AF: 0.151 AC: 2923 AN: 19416

Ashkenazi Jewish (ASJ) AF: 0.0610 AC: 1216 AN: 19926

East Asian (EAS) AF: 0.389 AC: 12336 AN: 31694

South Asian (SAS) AF: 0.0931 AC: 5629 AN: 60450

European-Finnish (FIN) AF: 0.0699 AC: 3492 AN: 49992

Middle Eastern (MID) AF: 0.0879 AC: 461 AN: 5242

European-Non Finnish (NFE) AF: 0.0515 AC: 54079 AN: 1050340

Other (OTH) AF: 0.0907 AC: 4910 AN: 54110

GnomAD4 genome AF: 0.136 AC: 20670 AN: 152004 Hom.: 2189 Cov.: 32 AF XY: 0.136 AC XY: 10136 AN XY: 74290

African (AFR) AF: 0.274 AC: 11368 AN: 41422

American (AMR) AF: 0.137 AC: 2098 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0548 AC: 190 AN: 3470

East Asian (EAS) AF: 0.333 AC: 1711 AN: 5138

South Asian (SAS) AF: 0.112 AC: 541 AN: 4812

European-Finnish (FIN) AF: 0.0686 AC: 727 AN: 10594

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0551 AC: 3743 AN: 67970

Other (OTH) AF: 0.106 AC: 223 AN: 2112

Alfa AF: 0.0836 Hom.: 4027

Bravo AF: 0.148

Asia WGS AF: 0.249 AC: 864 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.0
DANN	Benign	0.73
PhyloP100		0.76
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: rs16921669; hg19: chr9-4635232; COSMIC: COSV56305563; COSMIC: COSV56305563;