chr3-109013262-C-T

Variant names:

• chr3-109013262-C-T
• rs2197741
• NM_014429.4:c.1705-6171G>A

Variant summary

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

The NM_014429.4(MORC1):​c.1705-6171G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.899 in 152,120 control chromosomes in the GnomAD database, including 62,712 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 0.90 (62712 hom., cov: 31)
• Consequence: MORC1 NM_014429.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.449
• Publications: 2 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014429.4. 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
	MORC1	NM_014429.4	MANE Select	c.1705-6171G>A		intron	N/A	NP_055244.3	Q86VD1-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MORC1	ENST00000232603.10	TSL:1 MANE Select	c.1705-6171G>A		intron	N/A	ENSP00000232603.5	Q86VD1-1
	MORC1	ENST00000483760.1	TSL:2	c.1705-7947G>A		intron	N/A	ENSP00000417282.1	Q86VD1-2

Frequencies

GnomAD3 genomes AF: 0.900 AC: 136726 AN: 152002 Hom.: 62676 Cov.: 31

Gnomad AFR AF: 0.696

Gnomad AMI AF: 0.997

Gnomad AMR AF: 0.948

Gnomad ASJ AF: 0.959

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.973

Gnomad FIN AF: 0.990

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.980

Gnomad OTH AF: 0.912

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.899 AC: 136815 AN: 152120 Hom.: 62712 Cov.: 31 AF XY: 0.902 AC XY: 67113 AN XY: 74388

African (AFR) AF: 0.696 AC: 28823 AN: 41398

American (AMR) AF: 0.948 AC: 14503 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.959 AC: 3331 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5191 AN: 5192

South Asian (SAS) AF: 0.973 AC: 4700 AN: 4828

European-Finnish (FIN) AF: 0.990 AC: 10485 AN: 10594

Middle Eastern (MID) AF: 0.881 AC: 259 AN: 294

European-Non Finnish (NFE) AF: 0.980 AC: 66690 AN: 68032

Other (OTH) AF: 0.914 AC: 1926 AN: 2108

Alfa AF: 0.935 Hom.: 9071

Bravo AF: 0.888

Asia WGS AF: 0.967 AC: 3362 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.59
DANN	Benign	0.46
PhyloP100		-0.45
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2197741; hg19: chr3-108732109;