7-73645676-C-T

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MLXIPL	XM_047420437.1	c.-239+2070G>A		intron_variant	Intron 1 of 16		XP_047276393.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;