chr6-16158043-G-A

Variant names:

• chr6-16158043-G-A
• rs9367897
• XR_007059254.1:n.4914-3143G>A

Variant summary

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

The XR_007059254.1(MYLIP):​n.4914-3143G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.331 in 152,142 control chromosomes in the GnomAD database, including 10,383 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 0.33 (10383 hom., cov: 33)
• Consequence: MYLIP XR_007059254.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.52
• Publications: 3 publications found

Genes affected

MYLIP (HGNC:21155): (myosin regulatory light chain interacting protein) The ERM protein family members ezrin, radixin, and moesin are cytoskeletal effector proteins linking actin to membrane-bound proteins at the cell surface. Myosin regulatory light chain interacting protein (MYLIP) is a novel ERM-like protein that interacts with myosin regulatory light chain and inhibits neurite outgrowth. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.701 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: 0.331 AC: 50274 AN: 152024 Hom.: 10355 Cov.: 33

Gnomad AFR AF: 0.546

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.719

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.331 AC: 50366 AN: 152142 Hom.: 10383 Cov.: 33 AF XY: 0.330 AC XY: 24585 AN XY: 74388

African (AFR) AF: 0.546 AC: 22655 AN: 41484

American (AMR) AF: 0.310 AC: 4736 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.219 AC: 760 AN: 3472

East Asian (EAS) AF: 0.720 AC: 3728 AN: 5178

South Asian (SAS) AF: 0.257 AC: 1239 AN: 4824

European-Finnish (FIN) AF: 0.213 AC: 2261 AN: 10596

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.206 AC: 14030 AN: 67978

Other (OTH) AF: 0.310 AC: 654 AN: 2112

Alfa AF: 0.251 Hom.: 18190

Bravo AF: 0.352

Asia WGS AF: 0.522 AC: 1813 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	14
DANN	Benign	0.82
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs9367897; hg19: chr6-16158274;