chr19-51693156-G-A

Variant names:

• chr19-51693156-G-A
• rs41275794
• ENST00000602324.1:n.301C>T

Variant summary

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

The ENST00000602324.1(SPACA6-AS1):​n.301C>T 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 0.0251 in 445,190 control chromosomes in the GnomAD database, including 267 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 0.022 (72 hom., cov: 32)
  • Exomes 𝑓: 0.027 (195 hom.)
• Consequence: SPACA6-AS1 ENST00000602324.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00
• Publications: 19 publications found

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]

MIR125A (HGNC:31505): (microRNA 125a) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]

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 (EAS) allele frequency at 95% confidence interval = 0.0915 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000602324.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPACA6-AS1	NR_108100.1		n.301C>T		non_coding_transcript_exon	Exon 1 of 2
	SPACA6	NM_001316994.2		c.92-1322G>A		intron	N/A	NP_001303923.1
	SPACA6	NM_001316972.2	MANE Select	c.-371G>A		upstream_gene	N/A	NP_001303901.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPACA6-AS1	ENST00000602324.1	TSL:2	n.301C>T		non_coding_transcript_exon	Exon 1 of 2
	SPACA6	ENST00000710615.1		c.-41-1322G>A		intron	N/A	ENSP00000518379.1
	SPACA6	ENST00000646845.1		c.368-1322G>A		intron	N/A	ENSP00000496692.1

Frequencies

GnomAD3 genomes AF: 0.0223 AC: 3381 AN: 151902 Hom.: 71 Cov.: 32

Gnomad AFR AF: 0.00561

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0120

Gnomad ASJ AF: 0.0135

Gnomad EAS AF: 0.0990

Gnomad SAS AF: 0.00787

Gnomad FIN AF: 0.0348

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0287

Gnomad OTH AF: 0.0129

GnomAD4 exome AF: 0.0265 AC: 7777 AN: 293170 Hom.: 195 Cov.: 0 AF XY: 0.0249 AC XY: 3919 AN XY: 157076

African (AFR) AF: 0.00432 AC: 35 AN: 8110

American (AMR) AF: 0.00577 AC: 97 AN: 16806

Ashkenazi Jewish (ASJ) AF: 0.0124 AC: 100 AN: 8084

East Asian (EAS) AF: 0.103 AC: 1458 AN: 14134

South Asian (SAS) AF: 0.00954 AC: 428 AN: 44866

European-Finnish (FIN) AF: 0.0315 AC: 934 AN: 29624

Middle Eastern (MID) AF: 0.00401 AC: 11 AN: 2742

European-Non Finnish (NFE) AF: 0.0285 AC: 4378 AN: 153874

Other (OTH) AF: 0.0225 AC: 336 AN: 14930

GnomAD4 genome AF: 0.0223 AC: 3389 AN: 152020 Hom.: 72 Cov.: 32 AF XY: 0.0226 AC XY: 1677 AN XY: 74312

African (AFR) AF: 0.00560 AC: 232 AN: 41444

American (AMR) AF: 0.0120 AC: 183 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0135 AC: 47 AN: 3472

East Asian (EAS) AF: 0.0986 AC: 509 AN: 5162

South Asian (SAS) AF: 0.00808 AC: 39 AN: 4824

European-Finnish (FIN) AF: 0.0348 AC: 368 AN: 10572

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0287 AC: 1954 AN: 67968

Other (OTH) AF: 0.0171 AC: 36 AN: 2108

Alfa AF: 0.0154 Hom.: 5

Bravo AF: 0.0200

Asia WGS AF: 0.0510 AC: 177 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.7
DANN	Benign	0.69
PhyloP100		-1.0
PromoterAI		-0.021	Neutral

Splicing

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

Other links and lift over

dbSNP: rs41275794; hg19: chr19-52196409;