3-109084487-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_014429.4(MORC1):​c.689+8949A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.881 in 152,110 control chromosomes in the GnomAD database, including 59,099 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 0.88 ( 59099 hom., cov: 32)

Consequence

MORC1
NM_014429.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.09
Variant links:
Genes affected
MORC1 (HGNC:7198): (MORC family CW-type zinc finger 1) This gene encodes the human homolog of mouse morc and like the mouse protein it is testis-specific. Mouse studies support a testis-specific function since only male knockout mice are infertile; infertility is the only apparent defect. These studies further support a role for this protein early in spermatogenesis, possibly by affecting entry into apoptosis because testis from knockout mice show greatly increased numbers of apoptotic cells. [provided by RefSeq, Jan 2009]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.906 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
MORC1NM_014429.4 linkc.689+8949A>C intron_variant ENST00000232603.10 NP_055244.3 Q86VD1-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
MORC1ENST00000232603.10 linkc.689+8949A>C intron_variant 1 NM_014429.4 ENSP00000232603.5 Q86VD1-1
MORC1ENST00000483760.1 linkc.689+8949A>C intron_variant 2 ENSP00000417282.1 Q86VD1-2

Frequencies

GnomAD3 genomes
AF:
0.881
AC:
133890
AN:
151994
Hom.:
59048
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.903
Gnomad AMI
AF:
0.877
Gnomad AMR
AF:
0.907
Gnomad ASJ
AF:
0.850
Gnomad EAS
AF:
0.927
Gnomad SAS
AF:
0.872
Gnomad FIN
AF:
0.891
Gnomad MID
AF:
0.873
Gnomad NFE
AF:
0.859
Gnomad OTH
AF:
0.881
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.881
AC:
133994
AN:
152110
Hom.:
59099
Cov.:
32
AF XY:
0.881
AC XY:
65553
AN XY:
74368
show subpopulations
Gnomad4 AFR
AF:
0.903
Gnomad4 AMR
AF:
0.907
Gnomad4 ASJ
AF:
0.850
Gnomad4 EAS
AF:
0.928
Gnomad4 SAS
AF:
0.870
Gnomad4 FIN
AF:
0.891
Gnomad4 NFE
AF:
0.859
Gnomad4 OTH
AF:
0.875
Alfa
AF:
0.877
Hom.:
7269
Bravo
AF:
0.884
Asia WGS
AF:
0.878
AC:
3050
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
1.0
DANN
Benign
0.75

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs4507260; hg19: chr3-108803334; API