ENST00000629499.2:n.241+14699C>G

Variant names:

• chr11-102656034-C-G
• rs1940041
• ENST00000629499.2:n.241+14699C>G

Variant summary

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

The ENST00000629499.2(ENSG00000281655):​n.241+14699C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.553 in 152,032 control chromosomes in the GnomAD database, including 23,363 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 0.55 (23363 hom., cov: 33)
• Consequence: ENSG00000281655 ENST00000629499.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.505
• Publications: 2 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.598 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MMP20-AS1	NR_183620.1	n.212+14699C>G		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000281655	ENST00000629499.2	n.241+14699C>G		intron_variant	Intron 1 of 4	3
ENSG00000281655	ENST00000702066.2	n.258+14699C>G		intron_variant	Intron 1 of 3
ENSG00000281655	ENST00000702510.2	n.251+14699C>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.553 AC: 84055 AN: 151914 Hom.: 23340 Cov.: 33

Gnomad AFR AF: 0.551

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.587

Gnomad ASJ AF: 0.521

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.598

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.536

Gnomad OTH AF: 0.536

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

GnomAD4 genome AF: 0.553 AC: 84127 AN: 152032 Hom.: 23363 Cov.: 33 AF XY: 0.558 AC XY: 41449 AN XY: 74304

African (AFR) AF: 0.551 AC: 22844 AN: 41482

American (AMR) AF: 0.587 AC: 8974 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.521 AC: 1803 AN: 3460

East Asian (EAS) AF: 0.615 AC: 3183 AN: 5172

South Asian (SAS) AF: 0.590 AC: 2842 AN: 4820

European-Finnish (FIN) AF: 0.598 AC: 6309 AN: 10552

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.536 AC: 36396 AN: 67946

Other (OTH) AF: 0.541 AC: 1143 AN: 2112

Alfa AF: 0.557 Hom.: 3006

Bravo AF: 0.552

Asia WGS AF: 0.594 AC: 2065 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.5
DANN	Benign	0.64
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs1940041; hg19: chr11-102526765;