rs1328641

Positions:

• chr13-36170892-C-T

Variant summary

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

The NM_017826.3(SOHLH2):​c.1001-105G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 1,498,676 control chromosomes in the GnomAD database, including 57,992 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 0.25 (5059 hom., cov: 33)
  • Exomes 𝑓: 0.28 (52933 hom.)
• Consequence: SOHLH2 NM_017826.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.171

Genes affected

SOHLH2 (HGNC:26026): (spermatogenesis and oogenesis specific basic helix-loop-helix 2) This gene encodes one of testis-specific transcription factors which are essential for spermatogenesis, oogenesis and folliculogenesis. This gene is located on chromosome 13. The proteins encoded by this gene and another testis-specific transcription factor, SOHLH1, can form heterodimers, in addition to homodimers. There is a read-through locus (GeneID: 100526761) that shares sequence identity with this gene and the upstream CCDC169 (GeneID: 728591). Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2013]

CCDC169-SOHLH2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.281 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SOHLH2	NM_017826.3	c.1001-105G>A		intron_variant		ENST00000379881.8
CCDC169-SOHLH2	NM_001198910.2	c.1232-105G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SOHLH2	ENST00000379881.8	c.1001-105G>A		intron_variant		1	NM_017826.3	P1

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37848 AN: 151970 Hom.: 5057 Cov.: 33

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.257

GnomAD4 exome AF: 0.278 AC: 374182 AN: 1346588 Hom.: 52933 AF XY: 0.279 AC XY: 184390 AN XY: 661438

Gnomad4 AFR exome AF: 0.154

Gnomad4 AMR exome AF: 0.216

Gnomad4 ASJ exome AF: 0.265

Gnomad4 EAS exome AF: 0.239

Gnomad4 SAS exome AF: 0.283

Gnomad4 FIN exome AF: 0.363

Gnomad4 NFE exome AF: 0.281

Gnomad4 OTH exome AF: 0.276

GnomAD4 genome AF: 0.249 AC: 37848 AN: 152088 Hom.: 5059 Cov.: 33 AF XY: 0.253 AC XY: 18825 AN XY: 74326

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.232

Gnomad4 ASJ AF: 0.274

Gnomad4 EAS AF: 0.220

Gnomad4 SAS AF: 0.294

Gnomad4 FIN AF: 0.383

Gnomad4 NFE AF: 0.283

Gnomad4 OTH AF: 0.254

Alfa AF: 0.272 Hom.: 4771

Bravo AF: 0.232

Asia WGS AF: 0.258 AC: 897 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	1.8
DANN	Benign	0.73

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

Publications

LitVar

Other links and lift over

dbSNP: rs1328641; hg19: chr13-36745029;