15-100349291-T-G

Position:

• chr15-100349291-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_028139.1(SPATA41):​n.1428A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.746 in 154,762 control chromosomes in the GnomAD database, including 43,908 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 0.75 (43128 hom., cov: 32)
  • Exomes 𝑓: 0.75 (780 hom.)
• Consequence: SPATA41 NR_028139.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0530

Genes affected

SPATA41 (HGNC:48613): (spermatogenesis associated 41)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.821 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SPATA41	NR_028139.1	n.1428A>C		non_coding_transcript_exon_variant	1/2
SPATA41	NR_028140.1	n.393+17A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SPATA41	ENST00000662214.1	n.1435A>C		non_coding_transcript_exon_variant	1/2
SPATA41	ENST00000560282.1	n.365A>C		non_coding_transcript_exon_variant	1/2	2
SPATA41	ENST00000647665.1	n.532A>C		non_coding_transcript_exon_variant	1/2
SPATA41	ENST00000558307.1	n.81+17A>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.747 AC: 113431 AN: 151934 Hom.: 43103 Cov.: 32

Gnomad AFR AF: 0.709

Gnomad AMI AF: 0.809

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.710

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.652

Gnomad FIN AF: 0.756

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.827

Gnomad OTH AF: 0.748

GnomAD4 exome AF: 0.749 AC: 2030 AN: 2710 Hom.: 780 Cov.: 0 AF XY: 0.755 AC XY: 1062 AN XY: 1406

Gnomad4 AFR exome AF: 0.705

Gnomad4 AMR exome AF: 0.625

Gnomad4 ASJ exome AF: 0.833

Gnomad4 SAS exome AF: 0.734

Gnomad4 FIN exome AF: 0.755

Gnomad4 NFE exome AF: 0.849

Gnomad4 OTH exome AF: 0.690

GnomAD4 genome AF: 0.746 AC: 113491 AN: 152052 Hom.: 43128 Cov.: 32 AF XY: 0.738 AC XY: 54840 AN XY: 74328

Gnomad4 AFR AF: 0.709

Gnomad4 AMR AF: 0.606

Gnomad4 ASJ AF: 0.710

Gnomad4 EAS AF: 0.488

Gnomad4 SAS AF: 0.652

Gnomad4 FIN AF: 0.756

Gnomad4 NFE AF: 0.827

Gnomad4 OTH AF: 0.741

Alfa AF: 0.795 Hom.: 64737

Bravo AF: 0.734

Asia WGS AF: 0.526 AC: 1832 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.4
DANN	Benign	0.32

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2289584; hg19: chr15-100889496;