rs9367897

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr6-16158043-G-A
• chr6-16158043-G-C
• chr6-16158043-G-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.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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYLIP	XR_007059254.1	n.4914-3143G>A		intron_variant	Intron 7 of 7
MYLIP	XR_007059255.1	n.4913+3742G>A		intron_variant	Intron 7 of 7
MYLIP	XR_007059257.1	n.1701-3143G>A		intron_variant	Intron 8 of 9

Ensembl

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

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 v4.3

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;