rs2011503

Positions:

• chr19-19333177-T-C
• chr19-19333177-T-G

Variant summary

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

The NM_015329.4(MAU2):​c.277-2541T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.842 in 152,078 control chromosomes in the GnomAD database, including 54,011 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 0.84 (54011 hom., cov: 31)
• Consequence: MAU2 NM_015329.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.57

Genes affected

MAU2 (HGNC:29140): (MAU2 sister chromatid cohesion factor) Enables protein N-terminus binding activity. Involved in cohesin loading and maintenance of mitotic sister chromatid cohesion. Located in chromatin and nuclear body. Part of Scc2-Scc4 cohesin loading complex. [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=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAU2	NM_015329.4	c.277-2541T>C		intron_variant		ENST00000262815.13	NP_056144.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAU2	ENST00000262815.13	c.277-2541T>C		intron_variant		1	NM_015329.4	ENSP00000262815	P1
MAU2	ENST00000609122.5	c.151-3993T>C		intron_variant		4		ENSP00000477034
MAU2	ENST00000586189.7	n.380-2541T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.842 AC: 127914 AN: 151960 Hom.: 53961 Cov.: 31

Gnomad AFR AF: 0.822

Gnomad AMI AF: 0.732

Gnomad AMR AF: 0.865

Gnomad ASJ AF: 0.794

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.882

Gnomad FIN AF: 0.898

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.830

Gnomad OTH AF: 0.804

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

GnomAD4 genome AF: 0.842 AC: 128019 AN: 152078 Hom.: 54011 Cov.: 31 AF XY: 0.846 AC XY: 62871 AN XY: 74338

Gnomad4 AFR AF: 0.823

Gnomad4 AMR AF: 0.865

Gnomad4 ASJ AF: 0.794

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.882

Gnomad4 FIN AF: 0.898

Gnomad4 NFE AF: 0.830

Gnomad4 OTH AF: 0.806

Alfa AF: 0.839 Hom.: 8671

Bravo AF: 0.839

Asia WGS AF: 0.947 AC: 3295 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.21
DANN	Benign	0.25

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: rs2011503; hg19: chr19-19443986;