rs2273747

Variant names:

• chr10-119831999-G-A
• rs2273747
• NM_001256378.2:c.1796+13C>T

Your query was ambiguous. Multiple possible variants found:

• chr10-119831999-G-A
• chr10-119831999-G-T

Variant summary

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

The NM_001256378.2(MCMBP):​c.1796+13C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 1,602,792 control chromosomes in the GnomAD database, including 30,832 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 0.17 (2288 hom., cov: 32)
  • Exomes 𝑓: 0.19 (28544 hom.)
• Consequence: MCMBP NM_001256378.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.724
• Publications: 17 publications found

Genes affected

MCMBP (HGNC:25782): (minichromosome maintenance complex binding protein) This gene encodes a protein which is a component of the hexameric minichromosome maintenance (MCM) complex which regulates initiation and elongation of DNA. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2012]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001256378.2. 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
	MCMBP	NM_001256378.2	MANE Select	c.1796+13C>T		intron	N/A	NP_001243307.1	A0A0S2Z5P5
	MCMBP	NM_024834.4		c.1802+13C>T		intron	N/A	NP_079110.1	Q9BTE3-1
	MCMBP	NM_001256379.2		c.1277+13C>T		intron	N/A	NP_001243308.1	Q9BTE3-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MCMBP	ENST00000369077.4	TSL:1 MANE Select	c.1796+13C>T		intron	N/A	ENSP00000358073.3	Q9BTE3-2
	MCMBP	ENST00000360003.7	TSL:2	c.1802+13C>T		intron	N/A	ENSP00000353098.3	Q9BTE3-1
	MCMBP	ENST00000966480.1		c.1802+13C>T		intron	N/A	ENSP00000636539.1

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25366 AN: 151990 Hom.: 2284 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.149

GnomAD2 exomes AF: 0.196 AC: 47653 AN: 243352 AF XY: 0.210

Gnomad AFR exome AF: 0.142

Gnomad AMR exome AF: 0.120

Gnomad ASJ exome AF: 0.196

Gnomad EAS exome AF: 0.185

Gnomad FIN exome AF: 0.154

Gnomad NFE exome AF: 0.173

Gnomad OTH exome AF: 0.187

GnomAD4 exome AF: 0.187 AC: 271047 AN: 1450684 Hom.: 28544 Cov.: 30 AF XY: 0.195 AC XY: 140835 AN XY: 721490

African (AFR) AF: 0.138 AC: 4535 AN: 32954

American (AMR) AF: 0.121 AC: 5118 AN: 42376

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 4818 AN: 25702

East Asian (EAS) AF: 0.182 AC: 7164 AN: 39422

South Asian (SAS) AF: 0.432 AC: 36521 AN: 84578

European-Finnish (FIN) AF: 0.153 AC: 8147 AN: 53226

Middle Eastern (MID) AF: 0.210 AC: 1199 AN: 5700

European-Non Finnish (NFE) AF: 0.173 AC: 191836 AN: 1106874

Other (OTH) AF: 0.196 AC: 11709 AN: 59852

GnomAD4 genome AF: 0.167 AC: 25382 AN: 152108 Hom.: 2288 Cov.: 32 AF XY: 0.170 AC XY: 12669 AN XY: 74358

African (AFR) AF: 0.142 AC: 5901 AN: 41466

American (AMR) AF: 0.132 AC: 2025 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 659 AN: 3470

East Asian (EAS) AF: 0.180 AC: 933 AN: 5178

South Asian (SAS) AF: 0.441 AC: 2122 AN: 4816

European-Finnish (FIN) AF: 0.151 AC: 1599 AN: 10562

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.171 AC: 11650 AN: 68000

Other (OTH) AF: 0.149 AC: 315 AN: 2116

Alfa AF: 0.186 Hom.: 1680

Bravo AF: 0.157

Asia WGS AF: 0.269 AC: 938 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.045
DANN	Benign	0.58
PhyloP100		-0.72
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs2273747; hg19: chr10-121591511; COSMIC: COSV62820243; COSMIC: COSV62820243;