chr1-58658874-A-G

Position:

• chr1-58658874-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.*1123T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.626 in 151,366 control chromosomes in the GnomAD database, including 29,907 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 0.63 (29907 hom., cov: 28)
  • Failed GnomAD Quality Control
• Consequence: MYSM1 NM_001085487.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.629

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]

MYSM1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.68 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYSM1	NM_001085487.3	c.*1123T>C		3_prime_UTR_variant	20/20	ENST00000472487.6	NP_001078956.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYSM1	ENST00000472487	c.*1123T>C		3_prime_UTR_variant	20/20	1	NM_001085487.3	ENSP00000418734.1

Frequencies

GnomAD3 genomes AF: 0.626 AC: 94725 AN: 151248 Hom.: 29867 Cov.: 28

Gnomad AFR AF: 0.687

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.621

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.637

Gnomad SAS AF: 0.610

Gnomad FIN AF: 0.712

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.571

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.626 AC: 94819 AN: 151366 Hom.: 29907 Cov.: 28 AF XY: 0.632 AC XY: 46684 AN XY: 73878

Gnomad4 AFR AF: 0.687

Gnomad4 AMR AF: 0.620

Gnomad4 ASJ AF: 0.518

Gnomad4 EAS AF: 0.637

Gnomad4 SAS AF: 0.609

Gnomad4 FIN AF: 0.712

Gnomad4 NFE AF: 0.587

Gnomad4 OTH AF: 0.572

Alfa AF: 0.595 Hom.: 12284

Bravo AF: 0.620

Asia WGS AF: 0.640 AC: 2224 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.0
DANN	Benign	0.69

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: rs232775; hg19: chr1-59124546;