rs9367897

Positions:

• chr6-16158043-G-A
• chr6-16158043-G-C
• chr6-16158043-G-T

Variant summary

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

The XR_007059254.1(MYLIP):​n.4914-3143G>A variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.52

Genes affected

MYLIP (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
MYLIP	XR_007059254.1	n.4914-3143G>A		intron_variant, non_coding_transcript_variant
MYLIP	XR_007059255.1	n.4913+3742G>A		intron_variant, non_coding_transcript_variant
MYLIP	XR_007059257.1	n.1701-3143G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.546

Gnomad4 AMR AF: 0.310

Gnomad4 ASJ AF: 0.219

Gnomad4 EAS AF: 0.720

Gnomad4 SAS AF: 0.257

Gnomad4 FIN AF: 0.213

Gnomad4 NFE AF: 0.206

Gnomad4 OTH AF: 0.310

Alfa AF: 0.230 Hom.: 9239

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9367897; hg19: chr6-16158274;