6-16130102-A-G

Position:

• chr6-16130102-A-G

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 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. Variant has been reported in Lovd as Benign (no stars).

• 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

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

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BP6: Variant 6-16130102-A-G is Benign according to our data. Variant chr6-16130102-A-G is described in Lovd as [Benign].
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.384 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYLIP	NM_013262.4	c.88-455A>G		intron_variant		ENST00000356840.8	NP_037394.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYLIP	ENST00000356840.8	c.88-455A>G		intron_variant		1	NM_013262.4	ENSP00000349298	P1
MYLIP	ENST00000349606.4	c.-266+693A>G		intron_variant		1		ENSP00000008686

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

Gnomad4 AFR AF: 0.332

Gnomad4 AMR AF: 0.222

Gnomad4 ASJ AF: 0.176

Gnomad4 EAS AF: 0.399

Gnomad4 SAS AF: 0.158

Gnomad4 FIN AF: 0.0971

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.192

Alfa AF: 0.124 Hom.: 1788

Bravo AF: 0.215

Asia WGS AF: 0.285 AC: 989 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	4.6
DANN	Benign	0.78

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

Publications

LitVar

Other links and lift over

dbSNP: rs909562; hg19: chr6-16130333;