6-16157030-C-T

Variant names:

• chr6-16157030-C-T
• rs6921316
• XR_007059254.1:n.4913+2729C>T

Variant summary

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

The XR_007059254.1(MYLIP):​n.4913+2729C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.328 in 152,126 control chromosomes in the GnomAD database, including 10,152 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 (10152 hom., cov: 32)
• Consequence: MYLIP XR_007059254.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.117
• Publications: 2 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.7 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: 0.327 AC: 49736 AN: 152008 Hom.: 10118 Cov.: 32

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.719

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.169

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.328 AC: 49840 AN: 152126 Hom.: 10152 Cov.: 32 AF XY: 0.327 AC XY: 24298 AN XY: 74364

African (AFR) AF: 0.536 AC: 22215 AN: 41474

American (AMR) AF: 0.309 AC: 4728 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.217 AC: 755 AN: 3472

East Asian (EAS) AF: 0.719 AC: 3718 AN: 5168

South Asian (SAS) AF: 0.257 AC: 1238 AN: 4822

European-Finnish (FIN) AF: 0.213 AC: 2263 AN: 10600

Middle Eastern (MID) AF: 0.182 AC: 53 AN: 292

European-Non Finnish (NFE) AF: 0.206 AC: 13985 AN: 67988

Other (OTH) AF: 0.301 AC: 636 AN: 2112

Alfa AF: 0.289 Hom.: 1250

Bravo AF: 0.347

Asia WGS AF: 0.524 AC: 1820 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.77
DANN	Benign	0.20
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs6921316; hg19: chr6-16157261;