rs10265216

Variant names:

• chr7-131215362-T-A
• rs10265216
• NM_001145354.2:c.29+72421T>A

Your query was ambiguous. Multiple possible variants found:

• chr7-131215362-T-A
• chr7-131215362-T-C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
MKLN1	NM_001145354.2	c.29+72421T>A		intron_variant	Intron 2 of 18		NP_001138826.1
MKLN1	XM_047420401.1	c.29+72421T>A		intron_variant	Intron 2 of 18		XP_047276357.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MKLN1	ENST00000421797.6	c.-179+72421T>A		intron_variant	Intron 2 of 18	2		ENSP00000398094.2
MKLN1	ENST00000416992.6	c.-179+12388T>A		intron_variant	Intron 3 of 7	3		ENSP00000387920.1

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

African (AFR) AF: 0.192 AC: 7989 AN: 41512

American (AMR) AF: 0.427 AC: 6532 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 821 AN: 3470

East Asian (EAS) AF: 0.287 AC: 1483 AN: 5174

South Asian (SAS) AF: 0.452 AC: 2182 AN: 4824

European-Finnish (FIN) AF: 0.286 AC: 3023 AN: 10568

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.310 AC: 21103 AN: 67986

Other (OTH) AF: 0.298 AC: 630 AN: 2116

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
PhyloP100		0.28
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs10265216; hg19: chr7-130900121;