chr1-48329435-A-T

Variant names:

• chr1-48329435-A-T
• rs6700461
• NM_019073.4:c.1195-23557T>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.1195-23557T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 152,086 control chromosomes in the GnomAD database, including 13,787 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 (13787 hom., cov: 32)
• Consequence: SPATA6 NM_019073.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.559
• Publications: 4 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.507 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPATA6	NM_019073.4	c.1195-23557T>A		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.1195-23557T>A		intron_variant	Intron 11 of 12	1	NM_019073.4	ENSP00000360913.3

Frequencies

GnomAD3 genomes AF: 0.401 AC: 60944 AN: 151968 Hom.: 13779 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.429

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.429

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

GnomAD4 genome AF: 0.401 AC: 60961 AN: 152086 Hom.: 13787 Cov.: 32 AF XY: 0.402 AC XY: 29886 AN XY: 74318

African (AFR) AF: 0.178 AC: 7385 AN: 41512

American (AMR) AF: 0.431 AC: 6587 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.603 AC: 2094 AN: 3472

East Asian (EAS) AF: 0.355 AC: 1840 AN: 5178

South Asian (SAS) AF: 0.433 AC: 2091 AN: 4830

European-Finnish (FIN) AF: 0.451 AC: 4765 AN: 10560

Middle Eastern (MID) AF: 0.531 AC: 155 AN: 292

European-Non Finnish (NFE) AF: 0.512 AC: 34757 AN: 67946

Other (OTH) AF: 0.425 AC: 896 AN: 2106

Alfa AF: 0.340 Hom.: 1006

Bravo AF: 0.388

Asia WGS AF: 0.420 AC: 1456 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.5
DANN	Benign	0.72
PhyloP100		0.56
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: rs6700461; hg19: chr1-48795107;