chr7-73602675-A-G

Variant names:

• chr7-73602675-A-G
• rs13226650
• NM_032951.3:c.902-2980T>C

Variant summary

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

The NM_032951.3(MLXIPL):​c.902-2980T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.184 in 151,594 control chromosomes in the GnomAD database, including 2,685 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 0.18 (2685 hom., cov: 31)
• Consequence: MLXIPL NM_032951.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30
• Publications: 40 publications found

Genes affected

MLXIPL (HGNC:12744): (MLX interacting protein like) This gene encodes a basic helix-loop-helix leucine zipper transcription factor of the Myc/Max/Mad superfamily. This protein forms a heterodimeric complex and binds and activates, in a glucose-dependent manner, carbohydrate response element (ChoRE) motifs in the promoters of triglyceride synthesis genes. The gene is deleted in Williams-Beuren syndrome, a multisystem developmental disorder caused by the deletion of contiguous genes at chromosome 7q11.23. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2015]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032951.3. 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
	MLXIPL	NM_032951.3	MANE Select	c.902-2980T>C		intron	N/A	NP_116569.1	Q9NP71-1
	MLXIPL	NM_032953.3		c.902-2980T>C		intron	N/A	NP_116571.1	Q9NP71-3
	MLXIPL	NM_032952.3		c.902-2980T>C		intron	N/A	NP_116570.1	Q9NP71-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MLXIPL	ENST00000313375.8	TSL:1 MANE Select	c.902-2980T>C		intron	N/A	ENSP00000320886.3	Q9NP71-1
	MLXIPL	ENST00000414749.6	TSL:1	c.902-2980T>C		intron	N/A	ENSP00000412330.2	Q9NP71-3
	MLXIPL	ENST00000429400.6	TSL:1	c.902-2980T>C		intron	N/A	ENSP00000406296.2	Q9NP71-2

Frequencies

GnomAD3 genomes AF: 0.184 AC: 27831 AN: 151478 Hom.: 2682 Cov.: 31

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.0986

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.163

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.184 AC: 27854 AN: 151594 Hom.: 2685 Cov.: 31 AF XY: 0.181 AC XY: 13370 AN XY: 74030

African (AFR) AF: 0.221 AC: 9141 AN: 41346

American (AMR) AF: 0.131 AC: 2000 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 576 AN: 3464

East Asian (EAS) AF: 0.0991 AC: 501 AN: 5058

South Asian (SAS) AF: 0.102 AC: 487 AN: 4790

European-Finnish (FIN) AF: 0.159 AC: 1680 AN: 10550

Middle Eastern (MID) AF: 0.156 AC: 45 AN: 288

European-Non Finnish (NFE) AF: 0.191 AC: 12938 AN: 67832

Other (OTH) AF: 0.165 AC: 346 AN: 2102

Alfa AF: 0.185 Hom.: 6767

Bravo AF: 0.182

Asia WGS AF: 0.120 AC: 419 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.3
DANN	Benign	0.53
PhyloP100		-1.3
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: rs13226650; hg19: chr7-73017005;