chr11-102641030-G-C

Variant names:

• chr11-102641030-G-C
• rs7109663
• ENST00000629499.2:n.-65G>C

Variant summary

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

The ENST00000629499.2(ENSG00000281655):​n.-65G>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.342 in 152,056 control chromosomes in the GnomAD database, including 9,187 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 0.34 (9187 hom., cov: 32)
• Consequence: ENSG00000281655 ENST00000629499.2 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.366
• Publications: 1 publications found

Genes affected

ENSG00000281655 (HGNC:):

MMP20-AS1 (HGNC:56362): (MMP20 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000629499.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MMP20-AS1	NR_183620.1		n.-94G>C		upstream_gene	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000281655	ENST00000629499.2	TSL:3	n.-65G>C		upstream_gene	N/A
	ENSG00000281655	ENST00000702066.2		n.-48G>C		upstream_gene	N/A
	ENSG00000281655	ENST00000702510.2		n.-55G>C		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.342 AC: 51985 AN: 151938 Hom.: 9180 Cov.: 32

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.395

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.342 AC: 52008 AN: 152056 Hom.: 9187 Cov.: 32 AF XY: 0.345 AC XY: 25651 AN XY: 74334

African (AFR) AF: 0.258 AC: 10684 AN: 41482

American (AMR) AF: 0.366 AC: 5597 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.326 AC: 1132 AN: 3468

East Asian (EAS) AF: 0.314 AC: 1629 AN: 5184

South Asian (SAS) AF: 0.404 AC: 1948 AN: 4820

European-Finnish (FIN) AF: 0.425 AC: 4488 AN: 10550

Middle Eastern (MID) AF: 0.390 AC: 114 AN: 292

European-Non Finnish (NFE) AF: 0.373 AC: 25379 AN: 67964

Other (OTH) AF: 0.350 AC: 735 AN: 2102

Alfa AF: 0.360 Hom.: 1257

Bravo AF: 0.333

Asia WGS AF: 0.356 AC: 1237 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.81
DANN	Benign	0.68
PhyloP100		-0.37

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7109663;

hg19: chr11-102511761;