chr6-16156573-T-C

Variant names:

• chr6-16156573-T-C
• rs7742617
• XR_007059254.1:n.4913+2272T>C

Variant summary

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

The XR_007059254.1(MYLIP):​n.4913+2272T>C variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.134
• 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=-0.92).
• 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 rank	MANE	Protein	UniProt
MYLIP	XR_007059254.1	n.4913+2272T>C		intron_variant	Intron 7 of 7
MYLIP	XR_007059255.1	n.4913+2272T>C		intron_variant	Intron 7 of 7
MYLIP	XR_007059257.1	n.1700+2272T>C		intron_variant	Intron 8 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.525 AC: 21745 AN: 41428

American (AMR) AF: 0.309 AC: 4724 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.217 AC: 753 AN: 3470

East Asian (EAS) AF: 0.720 AC: 3719 AN: 5162

South Asian (SAS) AF: 0.257 AC: 1236 AN: 4802

European-Finnish (FIN) AF: 0.214 AC: 2261 AN: 10574

Middle Eastern (MID) AF: 0.182 AC: 53 AN: 292

European-Non Finnish (NFE) AF: 0.207 AC: 14049 AN: 67968

Other (OTH) AF: 0.303 AC: 640 AN: 2112

Alfa AF: 0.260 Hom.: 11930

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
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs7742617; hg19: chr6-16156804;