rs10265216

chr7-131215362-T-Achr7-131215362-T-C

Variant summary

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

The NM_001145354.2(MKLN1):c.29+72421T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 152,136 control chromosomes in the GnomAD database, including 6,800 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 0.29 (6800 hom., cov: 33)
• Consequence: MKLN1 NM_001145354.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.283

Genes affected

MKLN1 (HGNC:7109): (muskelin 1) Muskelin is an intracellular protein that acts as a mediator of cell spreading and cytoskeletal responses to the extracellular matrix component thrombospondin I (MIM 188060) (Adams et al., 1998 [PubMed 9724633]).[supplied by OMIM, Mar 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MKLN1	NM_001145354.2	c.29+72421T>A		intron_variant
MKLN1	XM_047420401.1	c.29+72421T>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MKLN1	ENST00000416992.6	c.-179+12388T>A		intron_variant		3
MKLN1	ENST00000421797.6	c.-179+72421T>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.290 AC: 44066 AN: 152018 Hom.: 6789 Cov.: 33

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.290 AC: 44112 AN: 152136 Hom.: 6800 Cov.: 33 AF XY: 0.294 AC XY: 21872 AN XY: 74380

Gnomad4 AFR AF: 0.192

Gnomad4 AMR AF: 0.427

Gnomad4 ASJ AF: 0.237

Gnomad4 EAS AF: 0.287

Gnomad4 SAS AF: 0.452

Gnomad4 FIN AF: 0.286

Gnomad4 NFE AF: 0.310

Gnomad4 OTH AF: 0.298

Alfa AF: 0.286 Hom.: 3550

Bravo AF: 0.292

Asia WGS AF: 0.412 AC: 1432 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	4.1
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10265216; hg19: chr7-130900121;