rs8112073

Positions:

• chr19-51692513-G-A
• chr19-51692513-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NR_108100.1(SPACA6-AS1):​n.823+121C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00383 in 434,878 control chromosomes in the GnomAD database, including 18 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 0.0091 (15 hom., cov: 32)
  • Exomes 𝑓: 0.0010 (3 hom.)
• Consequence: SPACA6-AS1 NR_108100.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.57

Genes affected

SPACA6-AS1 (HGNC:49383): (SPACA6 antisense RNA 1)

SPACA6 (HGNC:27113): (sperm acrosome associated 6) Predicted to be involved in fusion of sperm to egg plasma membrane involved in single fertilization. Predicted to be located in acrosomal vesicle. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00911 (1385/152064) while in subpopulation AFR AF= 0.0312 (1295/41484). AF 95% confidence interval is 0.0298. There are 15 homozygotes in gnomad4. There are 637 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 15 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SPACA6-AS1	NR_108100.1	n.823+121C>T		intron_variant, non_coding_transcript_variant
SPACA6	NM_001316994.2	c.92-1965G>A		intron_variant
SPACA6	XM_017026300.3	c.-41-1965G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPACA6-AS1	ENST00000602324.1	n.823+121C>T		intron_variant, non_coding_transcript_variant		2
SPACA6	ENST00000646845.1	c.368-1965G>A		intron_variant
SPACA6	ENST00000710615.1	c.-41-1965G>A		intron_variant				A2

Frequencies

GnomAD3 genomes AF: 0.00904 AC: 1374 AN: 151946 Hom.: 13 Cov.: 32

Gnomad AFR AF: 0.0310

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00380

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.000265

Gnomad OTH AF: 0.00671

GnomAD4 exome AF: 0.000997 AC: 282 AN: 282814 Hom.: 3 AF XY: 0.000837 AC XY: 136 AN XY: 162536

Gnomad4 AFR exome AF: 0.0305

Gnomad4 AMR exome AF: 0.00260

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000742

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000125

Gnomad4 OTH exome AF: 0.00224

GnomAD4 genome AF: 0.00911 AC: 1385 AN: 152064 Hom.: 15 Cov.: 32 AF XY: 0.00857 AC XY: 637 AN XY: 74342

Gnomad4 AFR AF: 0.0312

Gnomad4 AMR AF: 0.00373

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000265

Gnomad4 OTH AF: 0.00664

Alfa AF: 0.000374 Hom.: 0

Bravo AF: 0.0107

Asia WGS AF: 0.00404 AC: 14 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.9
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8112073; hg19: chr19-52195766;