chr15-100349291-T-G

Variant names:

• chr15-100349291-T-G
• rs2289584
• ENST00000560282.1:n.365A>C

Variant summary

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

The ENST00000560282.1(SPATA41):​n.365A>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 ENST00000560282.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0530
• Publications: 10 publications found

Genes affected

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

ENSG00000295388 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000560282.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPATA41	NR_028139.1		n.1428A>C		non_coding_transcript_exon	Exon 1 of 2
	SPATA41	NR_028140.1		n.393+17A>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPATA41	ENST00000560282.1	TSL:2	n.365A>C		non_coding_transcript_exon	Exon 1 of 2
	SPATA41	ENST00000647665.1		n.532A>C		non_coding_transcript_exon	Exon 1 of 2
	SPATA41	ENST00000662214.1		n.1435A>C		non_coding_transcript_exon	Exon 1 of 2

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

African (AFR) AF: 0.705 AC: 55 AN: 78

American (AMR) AF: 0.625 AC: 5 AN: 8

Ashkenazi Jewish (ASJ) AF: 0.833 AC: 5 AN: 6

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.734 AC: 69 AN: 94

European-Finnish (FIN) AF: 0.755 AC: 326 AN: 432

Middle Eastern (MID) AF: 0.742 AC: 1213 AN: 1634

European-Non Finnish (NFE) AF: 0.849 AC: 219 AN: 258

Other (OTH) AF: 0.690 AC: 138 AN: 200

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

African (AFR) AF: 0.709 AC: 29399 AN: 41456

American (AMR) AF: 0.606 AC: 9269 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.710 AC: 2463 AN: 3470

East Asian (EAS) AF: 0.488 AC: 2511 AN: 5148

South Asian (SAS) AF: 0.652 AC: 3136 AN: 4808

European-Finnish (FIN) AF: 0.756 AC: 8000 AN: 10582

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.827 AC: 56197 AN: 67986

Other (OTH) AF: 0.741 AC: 1561 AN: 2108

Alfa AF: 0.789 Hom.: 79734

Bravo AF: 0.734

Asia WGS AF: 0.526 AC: 1832 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.4
DANN	Benign	0.32
PhyloP100		0.053

Splicing

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

Other links and lift over

dbSNP: rs2289584; hg19: chr15-100889496;