rs7777102

Variant names:

• chr7-73643687-A-G
• rs7777102
• XM_047420437.1:c.-239+4059T>C

Your query was ambiguous. Multiple possible variants found:

• chr7-73643687-A-G
• chr7-73643687-A-T

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+4059T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 152,078 control chromosomes in the GnomAD database, including 2,174 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 0.16 (2174 hom., cov: 31)
• Consequence: MLXIPL XM_047420437.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.176
• Publications: 13 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.246 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.158 AC: 23958 AN: 151960 Hom.: 2158 Cov.: 31

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.0637

Gnomad AMR AF: 0.0909

Gnomad ASJ AF: 0.0937

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.0992

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.158 AC: 24002 AN: 152078 Hom.: 2174 Cov.: 31 AF XY: 0.156 AC XY: 11617 AN XY: 74352

African (AFR) AF: 0.250 AC: 10365 AN: 41460

American (AMR) AF: 0.0906 AC: 1384 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0937 AC: 325 AN: 3468

East Asian (EAS) AF: 0.187 AC: 967 AN: 5178

South Asian (SAS) AF: 0.0993 AC: 479 AN: 4824

European-Finnish (FIN) AF: 0.122 AC: 1290 AN: 10576

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.130 AC: 8819 AN: 67984

Other (OTH) AF: 0.128 AC: 271 AN: 2116

Alfa AF: 0.132 Hom.: 4716

Bravo AF: 0.158

Asia WGS AF: 0.148 AC: 516 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.2
DANN	Benign	0.71
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs7777102; hg19: chr7-73058017; COSMIC: COSV64448166;