chr6-16161194-A-G

Variant names:

• chr6-16161194-A-G
• rs6924995
• ENST00000407522.1:n.269A>G

Variant summary

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

The XR_007059254.1(MYLIP):​n.4922A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 242,378 control chromosomes in the GnomAD database, including 15,063 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 0.34 (11146 hom., cov: 32)
  • Exomes 𝑓: 0.26 (3917 hom.)
• Consequence: MYLIP XR_007059254.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0530
• Publications: 12 publications found

Genes affected

PERPP3 (HGNC:56913):

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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.708 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000407522.1. You can select a different transcript below to see updated ACMG assignments.

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
	PERPP3	ENST00000407522.1	TSL:6	n.269A>G		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.340 AC: 51672 AN: 151952 Hom.: 11106 Cov.: 32

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.727

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.307

GnomAD4 exome AF: 0.260 AC: 23482 AN: 90308 Hom.: 3917 Cov.: 0 AF XY: 0.253 AC XY: 13795 AN XY: 54550

African (AFR) AF: 0.592 AC: 1616 AN: 2732

American (AMR) AF: 0.339 AC: 1749 AN: 5158

Ashkenazi Jewish (ASJ) AF: 0.197 AC: 271 AN: 1374

East Asian (EAS) AF: 0.731 AC: 3193 AN: 4368

South Asian (SAS) AF: 0.235 AC: 3267 AN: 13926

European-Finnish (FIN) AF: 0.235 AC: 925 AN: 3940

Middle Eastern (MID) AF: 0.154 AC: 109 AN: 710

European-Non Finnish (NFE) AF: 0.209 AC: 11171 AN: 53498

Other (OTH) AF: 0.257 AC: 1181 AN: 4602

GnomAD4 genome AF: 0.341 AC: 51784 AN: 152070 Hom.: 11146 Cov.: 32 AF XY: 0.340 AC XY: 25250 AN XY: 74350

African (AFR) AF: 0.578 AC: 23953 AN: 41464

American (AMR) AF: 0.314 AC: 4797 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.220 AC: 762 AN: 3466

East Asian (EAS) AF: 0.728 AC: 3757 AN: 5162

South Asian (SAS) AF: 0.258 AC: 1239 AN: 4808

European-Finnish (FIN) AF: 0.214 AC: 2261 AN: 10572

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.207 AC: 14047 AN: 67992

Other (OTH) AF: 0.315 AC: 665 AN: 2110

Alfa AF: 0.259 Hom.: 20953

Bravo AF: 0.362

Asia WGS AF: 0.528 AC: 1834 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.0
DANN	Benign	0.35
PhyloP100		0.053

Splicing

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

Other links and lift over

dbSNP: rs6924995; hg19: chr6-16161425;