rs644955

chr1-54702411-C-T

Variant summary

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

The NM_001039464.4(MROH7):c.3441+166C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.565 in 151,986 control chromosomes in the GnomAD database, including 25,033 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 0.57 (25033 hom., cov: 32)
• Consequence: MROH7 NM_001039464.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.908

Genes affected

MROH7 (HGNC:24802): (maestro heat like repeat family member 7) Located in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

MROH7-TTC4 (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 (EAS) allele frequency at 95% confidence interval = 0.739 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MROH7	NM_001039464.4	c.3441+166C>T		intron_variant		ENST00000421030.7
MROH7-TTC4	NR_037639.2	n.3975+166C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MROH7	ENST00000421030.7	c.3441+166C>T		intron_variant		2	NM_001039464.4	P2

Frequencies

GnomAD3 genomes AF: 0.565 AC: 85812 AN: 151868 Hom.: 24997 Cov.: 32

Gnomad AFR AF: 0.690

Gnomad AMI AF: 0.583

Gnomad AMR AF: 0.559

Gnomad ASJ AF: 0.498

Gnomad EAS AF: 0.758

Gnomad SAS AF: 0.629

Gnomad FIN AF: 0.508

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.551

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

GnomAD4 genome AF: 0.565 AC: 85913 AN: 151986 Hom.: 25033 Cov.: 32 AF XY: 0.570 AC XY: 42318 AN XY: 74298

Gnomad4 AFR AF: 0.690

Gnomad4 AMR AF: 0.559

Gnomad4 ASJ AF: 0.498

Gnomad4 EAS AF: 0.759

Gnomad4 SAS AF: 0.629

Gnomad4 FIN AF: 0.508

Gnomad4 NFE AF: 0.484

Gnomad4 OTH AF: 0.551

Alfa AF: 0.501 Hom.: 25604

Bravo AF: 0.573

Asia WGS AF: 0.660 AC: 2293 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	0.16
Dann	Benign	0.66

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: rs644955; hg19: chr1-55168084; COSMIC: COSV59869903; COSMIC: COSV59869903;