rs799160

chr7-73645676-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

MLXIPL (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
MLXIPL	XM_047420437.1	c.-239+2070G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.400

Gnomad4 AMR AF: 0.589

Gnomad4 ASJ AF: 0.537

Gnomad4 EAS AF: 0.726

Gnomad4 SAS AF: 0.732

Gnomad4 FIN AF: 0.578

Gnomad4 NFE AF: 0.488

Gnomad4 OTH AF: 0.517

Alfa AF: 0.502 Hom.: 8713

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs799160; hg19: chr7-73060006;