chr6-16130102-A-G

Variant names:

• chr6-16130102-A-G
• rs909562
• NM_013262.4:c.88-455A>G

Variant summary

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

The NM_013262.4(MYLIP):​c.88-455A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 152,054 control chromosomes in the GnomAD database, including 3,778 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 0.19 (3778 hom., cov: 32)
• Consequence: MYLIP NM_013262.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.648
• Publications: 6 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=-0.64).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.384 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_013262.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYLIP	NM_013262.4	MANE Select	c.88-455A>G		intron	N/A	NP_037394.2
	MYLIP	NM_001436627.1		c.88-455A>G		intron	N/A	NP_001423556.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYLIP	ENST00000356840.8	TSL:1 MANE Select	c.88-455A>G		intron	N/A	ENSP00000349298.3
	MYLIP	ENST00000349606.5	TSL:1	n.87+693A>G		intron	N/A	ENSP00000008686.6
	MYLIP	ENST00000718320.1		c.88-455A>G		intron	N/A	ENSP00000520754.1

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29529 AN: 151936 Hom.: 3765 Cov.: 32

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.0971

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.194 AC: 29570 AN: 152054 Hom.: 3778 Cov.: 32 AF XY: 0.193 AC XY: 14376 AN XY: 74336

African (AFR) AF: 0.332 AC: 13784 AN: 41470

American (AMR) AF: 0.222 AC: 3400 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 610 AN: 3468

East Asian (EAS) AF: 0.399 AC: 2059 AN: 5164

South Asian (SAS) AF: 0.158 AC: 762 AN: 4808

European-Finnish (FIN) AF: 0.0971 AC: 1028 AN: 10584

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7266 AN: 67956

Other (OTH) AF: 0.192 AC: 406 AN: 2112

Alfa AF: 0.133 Hom.: 2741

Bravo AF: 0.215

Asia WGS AF: 0.285 AC: 989 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	4.6
DANN	Benign	0.78
PhyloP100		-0.65
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs909562; hg19: chr6-16130333;