rs1940471

Variant names:

• chr11-102669761-C-T
• rs1940471
• ENST00000629499.2:n.242-7942C>T

Variant summary

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

The ENST00000629499.2(ENSG00000281655):​n.242-7942C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0462 in 152,156 control chromosomes in the GnomAD database, including 459 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 0.046 (459 hom., cov: 33)
• Consequence: ENSG00000281655 ENST00000629499.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.493
• 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.142 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MMP20-AS1	NR_183620.1	n.213-7942C>T		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000281655	ENST00000629499.2	n.242-7942C>T		intron_variant	Intron 1 of 4	3
ENSG00000281655	ENST00000702066.2	n.259-7942C>T		intron_variant	Intron 1 of 3
ENSG00000281655	ENST00000702510.2	n.252-7942C>T		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.0462 AC: 7022 AN: 152038 Hom.: 461 Cov.: 33

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0211

Gnomad ASJ AF: 0.00721

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000621

Gnomad FIN AF: 0.00801

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.00750

Gnomad OTH AF: 0.0258

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

GnomAD4 genome AF: 0.0462 AC: 7036 AN: 152156 Hom.: 459 Cov.: 33 AF XY: 0.0447 AC XY: 3328 AN XY: 74382

African (AFR) AF: 0.145 AC: 6028 AN: 41490

American (AMR) AF: 0.0211 AC: 322 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.00721 AC: 25 AN: 3466

East Asian (EAS) AF: 0.00 AC: 0 AN: 5188

South Asian (SAS) AF: 0.000621 AC: 3 AN: 4828

European-Finnish (FIN) AF: 0.00801 AC: 85 AN: 10606

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.00750 AC: 510 AN: 67980

Other (OTH) AF: 0.0255 AC: 54 AN: 2114

Alfa AF: 0.0237 Hom.: 92

Bravo AF: 0.0511

Asia WGS AF: 0.0120 AC: 43 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.85
DANN	Benign	0.27
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs1940471; hg19: chr11-102540492;