chr1-48403616-T-A

Variant names:

• chr1-48403616-T-A
• rs3738309
• NM_019073.4:c.486+186A>T

Variant summary

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

The NM_019073.4(SPATA6):​c.486+186A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.31 in 151,914 control chromosomes in the GnomAD database, including 8,970 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 0.31 (8970 hom., cov: 32)
• Consequence: SPATA6 NM_019073.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.160
• Publications: 5 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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.414 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPATA6	NM_019073.4	c.486+186A>T		intron_variant	Intron 6 of 12	ENST00000371847.8	NP_061946.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPATA6	ENST00000371847.8	c.486+186A>T		intron_variant	Intron 6 of 12	1	NM_019073.4	ENSP00000360913.3

Frequencies

GnomAD3 genomes AF: 0.310 AC: 47128 AN: 151796 Hom.: 8962 Cov.: 32

Gnomad AFR AF: 0.0773

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.352

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.310 AC: 47137 AN: 151914 Hom.: 8970 Cov.: 32 AF XY: 0.312 AC XY: 23163 AN XY: 74232

African (AFR) AF: 0.0771 AC: 3200 AN: 41482

American (AMR) AF: 0.352 AC: 5363 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1618 AN: 3466

East Asian (EAS) AF: 0.352 AC: 1812 AN: 5148

South Asian (SAS) AF: 0.358 AC: 1719 AN: 4806

European-Finnish (FIN) AF: 0.364 AC: 3831 AN: 10534

Middle Eastern (MID) AF: 0.441 AC: 128 AN: 290

European-Non Finnish (NFE) AF: 0.418 AC: 28403 AN: 67914

Other (OTH) AF: 0.331 AC: 698 AN: 2108

Alfa AF: 0.365 Hom.: 1404

Bravo AF: 0.298

Asia WGS AF: 0.376 AC: 1306 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.3
DANN	Benign	0.74
PhyloP100		0.16
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: rs3738309; hg19: chr1-48869288; COSMIC: COSV107481124; COSMIC: COSV107481124;