rs232795

chr1-58667596-A-G

Variant summary

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

The NM_001085487.3(MYSM1):c.1842+251T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 151,564 control chromosomes in the GnomAD database, including 6,159 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 0.27 (6159 hom., cov: 30)
• Consequence: MYSM1 NM_001085487.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.355

Genes affected

MYSM1 (HGNC:29401): (Myb like, SWIRM and MPN domains 1) Enables histone binding activity; peptidase activity; and transcription coactivator activity. Involved in several processes, including chromatin remodeling; monoubiquitinated histone H2A deubiquitination; and positive regulation of transcription by RNA polymerase II. Located in nucleolus and nucleoplasm. Part of protein-containing complex. Implicated in diabetic retinopathy. [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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.404 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYSM1	NM_001085487.3	c.1842+251T>C		intron_variant		ENST00000472487.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYSM1	ENST00000472487.6	c.1842+251T>C		intron_variant		1	NM_001085487.3	P2

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40335 AN: 151446 Hom.: 6140 Cov.: 30

Gnomad AFR AF: 0.408

Gnomad AMI AF: 0.0582

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.150

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.267 AC: 40402 AN: 151564 Hom.: 6159 Cov.: 30 AF XY: 0.273 AC XY: 20208 AN XY: 73994

Gnomad4 AFR AF: 0.409

Gnomad4 AMR AF: 0.243

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.238

Gnomad4 SAS AF: 0.281

Gnomad4 FIN AF: 0.356

Gnomad4 NFE AF: 0.181

Gnomad4 OTH AF: 0.245

Alfa AF: 0.206 Hom.: 1656

Bravo AF: 0.262

Asia WGS AF: 0.278 AC: 966 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	7.0
Dann	Benign	0.29

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: rs232795; hg19: chr1-59133268;