chr1-48342131-A-G

Variant names:

• chr1-48342131-A-G
• rs12085824
• NM_019073.4:c.1194+13539T>C

Variant summary

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

The NM_019073.4(SPATA6):​c.1194+13539T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.4 in 152,092 control chromosomes in the GnomAD database, including 12,883 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 0.40 (12883 hom., cov: 32)
• Consequence: SPATA6 NM_019073.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.222
• Publications: 2 publications found

Genes affected

SPATA6 (HGNC:18309): (spermatogenesis associated 6) Predicted to enable myosin light chain binding activity. Predicted to be involved in motile cilium assembly and spermatogenesis. Predicted to be located in extracellular region. Predicted to be active 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPATA6	NM_019073.4	c.1194+13539T>C		intron_variant	Intron 11 of 12	ENST00000371847.8	NP_061946.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPATA6	ENST00000371847.8	c.1194+13539T>C		intron_variant	Intron 11 of 12	1	NM_019073.4	ENSP00000360913.3

Frequencies

GnomAD3 genomes AF: 0.400 AC: 60843 AN: 151974 Hom.: 12864 Cov.: 32

Gnomad AFR AF: 0.546

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.400 AC: 60898 AN: 152092 Hom.: 12883 Cov.: 32 AF XY: 0.395 AC XY: 29377 AN XY: 74356

African (AFR) AF: 0.546 AC: 22636 AN: 41466

American (AMR) AF: 0.403 AC: 6149 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.302 AC: 1046 AN: 3468

East Asian (EAS) AF: 0.188 AC: 973 AN: 5168

South Asian (SAS) AF: 0.363 AC: 1751 AN: 4830

European-Finnish (FIN) AF: 0.320 AC: 3388 AN: 10592

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.349 AC: 23740 AN: 67982

Other (OTH) AF: 0.374 AC: 790 AN: 2114

Alfa AF: 0.357 Hom.: 5770

Bravo AF: 0.412

Asia WGS AF: 0.279 AC: 972 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.0
DANN	Benign	0.67
PhyloP100		0.22
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: rs12085824; hg19: chr1-48807803; COSMIC: COSV64056749; COSMIC: COSV64056749;