rs799160

Variant names:

• chr7-73645676-C-T
• rs799160
• XM_047420437.1:c.-239+2070G>A

Variant summary

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

The XM_047420437.1(MLXIPL):​c.-239+2070G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.497 in 152,004 control chromosomes in the GnomAD database, including 19,417 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 0.50 (19417 hom., cov: 32)
• Consequence: MLXIPL XM_047420437.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.798
• Publications: 17 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.712 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.497 AC: 75468 AN: 151884 Hom.: 19399 Cov.: 32

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.726

Gnomad SAS AF: 0.731

Gnomad FIN AF: 0.578

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.497 AC: 75527 AN: 152004 Hom.: 19417 Cov.: 32 AF XY: 0.506 AC XY: 37606 AN XY: 74280

African (AFR) AF: 0.400 AC: 16588 AN: 41442

American (AMR) AF: 0.589 AC: 8993 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.537 AC: 1862 AN: 3470

East Asian (EAS) AF: 0.726 AC: 3755 AN: 5172

South Asian (SAS) AF: 0.732 AC: 3527 AN: 4820

European-Finnish (FIN) AF: 0.578 AC: 6102 AN: 10560

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.488 AC: 33199 AN: 67978

Other (OTH) AF: 0.517 AC: 1089 AN: 2108

Alfa AF: 0.507 Hom.: 12238

Bravo AF: 0.494

Asia WGS AF: 0.709 AC: 2464 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.82
DANN	Benign	0.53
PhyloP100		-0.80

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs799160; hg19: chr7-73060006;