chr1-48358484-A-T

Variant names:

• chr1-48358484-A-T
• rs932087
• NM_019073.4:c.1094+1102T>A

Variant summary

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

The NM_019073.4(SPATA6):​c.1094+1102T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.098 in 152,100 control chromosomes in the GnomAD database, including 877 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 0.098 (877 hom., cov: 32)
• Consequence: SPATA6 NM_019073.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.590
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.161 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPATA6	NM_019073.4	c.1094+1102T>A		intron_variant	Intron 10 of 12	ENST00000371847.8	NP_061946.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPATA6	ENST00000371847.8	c.1094+1102T>A		intron_variant	Intron 10 of 12	1	NM_019073.4	ENSP00000360913.3

Frequencies

GnomAD3 genomes AF: 0.0981 AC: 14911 AN: 151982 Hom.: 878 Cov.: 32

Gnomad AFR AF: 0.0513

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.0826

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.0110

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.0917

Gnomad MID AF: 0.121

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.0980 AC: 14913 AN: 152100 Hom.: 877 Cov.: 32 AF XY: 0.0964 AC XY: 7166 AN XY: 74350

African (AFR) AF: 0.0513 AC: 2128 AN: 41510

American (AMR) AF: 0.0824 AC: 1258 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 446 AN: 3470

East Asian (EAS) AF: 0.0108 AC: 56 AN: 5190

South Asian (SAS) AF: 0.171 AC: 826 AN: 4826

European-Finnish (FIN) AF: 0.0917 AC: 967 AN: 10542

Middle Eastern (MID) AF: 0.120 AC: 35 AN: 292

European-Non Finnish (NFE) AF: 0.130 AC: 8867 AN: 67980

Other (OTH) AF: 0.102 AC: 216 AN: 2108

Alfa AF: 0.115 Hom.: 131

Bravo AF: 0.0929

Asia WGS AF: 0.0830 AC: 290 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	1.4
DANN	Benign	0.46
PhyloP100		-0.59
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: rs932087; hg19: chr1-48824156;