6-16158632-A-G

Variant names:

• chr6-16158632-A-G
• rs9349997
• XR_007059254.1:n.4914-2554A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007059254.1(MYLIP):​n.4914-2554A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 152,066 control chromosomes in the GnomAD database, including 9,811 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 0.32 (9811 hom., cov: 32)
• Consequence: MYLIP XR_007059254.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.392

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.701 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYLIP	XR_007059254.1	n.4914-2554A>G		intron_variant	Intron 7 of 7
MYLIP	XR_007059255.1	n.4913+4331A>G		intron_variant	Intron 7 of 7
MYLIP	XR_007059257.1	n.1701-2554A>G		intron_variant	Intron 8 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.324 AC: 49192 AN: 151948 Hom.: 9785 Cov.: 32

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.720

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.324 AC: 49281 AN: 152066 Hom.: 9811 Cov.: 32 AF XY: 0.324 AC XY: 24057 AN XY: 74314

Gnomad4 AFR AF: 0.523

Gnomad4 AMR AF: 0.308

Gnomad4 ASJ AF: 0.219

Gnomad4 EAS AF: 0.720

Gnomad4 SAS AF: 0.257

Gnomad4 FIN AF: 0.211

Gnomad4 NFE AF: 0.206

Gnomad4 OTH AF: 0.304

Alfa AF: 0.286 Hom.: 1227

Bravo AF: 0.344

Asia WGS AF: 0.520 AC: 1805 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.57
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9349997; hg19: chr6-16158863;