rs1863009

Variant names:

• chr7-131314416-A-G
• rs1863009
• ENST00000656389.1:n.1253T>C

Variant summary

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

The ENST00000656389.1(MKLN1-AS):​n.1253T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.809 in 151,980 control chromosomes in the GnomAD database, including 49,897 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 0.81 (49897 hom., cov: 29)
• Consequence: MKLN1-AS ENST00000656389.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792
• Publications: 5 publications found

Genes affected

MKLN1-AS (HGNC:40374): (MKLN1 antisense RNA)

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MKLN1	NM_001145354.2	c.30-61008A>G		intron_variant	Intron 2 of 18		NP_001138826.1
MKLN1-AS	NR_125364.1	n.923-3193T>C		intron_variant	Intron 4 of 5
MKLN1	XM_047420401.1	c.30-61008A>G		intron_variant	Intron 2 of 18		XP_047276357.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MKLN1-AS	ENST00000656389.1	n.1253T>C		non_coding_transcript_exon_variant	Exon 5 of 5
MKLN1-AS	ENST00000656518.1	n.1232T>C		non_coding_transcript_exon_variant	Exon 5 of 5
MKLN1	ENST00000421797.6	c.-178-61008A>G		intron_variant	Intron 2 of 18	2		ENSP00000398094.2

Frequencies

GnomAD3 genomes AF: 0.809 AC: 122870 AN: 151862 Hom.: 49857 Cov.: 29

Gnomad AFR AF: 0.866

Gnomad AMI AF: 0.596

Gnomad AMR AF: 0.822

Gnomad ASJ AF: 0.688

Gnomad EAS AF: 0.813

Gnomad SAS AF: 0.739

Gnomad FIN AF: 0.819

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.785

Gnomad OTH AF: 0.787

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

GnomAD4 genome AF: 0.809 AC: 122963 AN: 151980 Hom.: 49897 Cov.: 29 AF XY: 0.811 AC XY: 60193 AN XY: 74256

African (AFR) AF: 0.865 AC: 35883 AN: 41468

American (AMR) AF: 0.822 AC: 12553 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.688 AC: 2385 AN: 3468

East Asian (EAS) AF: 0.812 AC: 4188 AN: 5156

South Asian (SAS) AF: 0.738 AC: 3547 AN: 4804

European-Finnish (FIN) AF: 0.819 AC: 8636 AN: 10542

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.785 AC: 53369 AN: 67958

Other (OTH) AF: 0.787 AC: 1665 AN: 2116

Alfa AF: 0.800 Hom.: 6862

Bravo AF: 0.814

Asia WGS AF: 0.781 AC: 2720 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	4.1
DANN	Benign	0.60
PhyloP100		-0.79
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: rs1863009; hg19: chr7-130999175;