rs7742617

Positions:

• chr6-16156573-T-C

Variant summary

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

The XR_007059254.1(MYLIP):​n.4913+2272T>C 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 0.325 in 152,008 control chromosomes in the GnomAD database, including 9,904 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 (9904 hom., cov: 32)
• Consequence: MYLIP XR_007059254.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.134

Genes affected

MYLIP (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• 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.4913+2272T>C		intron_variant, non_coding_transcript_variant
MYLIP	XR_007059255.1	n.4913+2272T>C		intron_variant, non_coding_transcript_variant
MYLIP	XR_007059257.1	n.1700+2272T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49330 AN: 151890 Hom.: 9871 Cov.: 32

Gnomad AFR AF: 0.525

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.720

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.169

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.325 AC: 49429 AN: 152008 Hom.: 9904 Cov.: 32 AF XY: 0.325 AC XY: 24121 AN XY: 74318

Gnomad4 AFR AF: 0.525

Gnomad4 AMR AF: 0.309

Gnomad4 ASJ AF: 0.217

Gnomad4 EAS AF: 0.720

Gnomad4 SAS AF: 0.257

Gnomad4 FIN AF: 0.214

Gnomad4 NFE AF: 0.207

Gnomad4 OTH AF: 0.303

Alfa AF: 0.232 Hom.: 6235

Bravo AF: 0.345

Asia WGS AF: 0.524 AC: 1820 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7742617; hg19: chr6-16156804;