rs3809717

Variant names:

• chr17-39730733-C-A
• rs3809717
• NM_032339.5:c.-238G>T

Your query was ambiguous. Multiple possible variants found:

• chr17-39730733-C-A
• chr17-39730733-C-G
• chr17-39730733-C-T

Variant summary

Our verdict is Benign. The variant received -7 ACMG points: 1P and 8B. PP3 BA1

The NM_032339.5(MIEN1):​c.-238G>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 526,334 control chromosomes in the GnomAD database, including 20,315 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 0.23 (4710 hom., cov: 32)
  • Exomes 𝑓: 0.28 (15605 hom.)
• Consequence: MIEN1 NM_032339.5 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59
• Publications: 10 publications found

Genes affected

MIEN1 (HGNC:28230): (migration and invasion enhancer 1) Involved in negative regulation of apoptotic process; positive regulation of cell migration; and positive regulation of filopodium assembly. Located in several cellular components, including centriolar satellite; cytosol; and nucleoplasm. Is intrinsic component of the cytoplasmic side of the plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -7 ACMG points.

• PP3: Splicing predictors support a deleterious effect. Scorers claiming Pathogenic: max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.288 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032339.5. 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
	MIEN1	NM_032339.5	MANE Select	c.-238G>T		upstream_gene	N/A	NP_115715.3
	MIEN1	NM_001330206.2		c.-238G>T		upstream_gene	N/A	NP_001317135.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIEN1	ENST00000394231.8	TSL:1 MANE Select	c.-238G>T		upstream_gene	N/A	ENSP00000377778.3
	MIEN1	ENST00000935318.1		c.-238G>T		upstream_gene	N/A	ENSP00000605376.1
	MIEN1	ENST00000577810.1	TSL:3	c.-238G>T		upstream_gene	N/A	ENSP00000462998.1

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34332 AN: 152034 Hom.: 4710 Cov.: 32

Gnomad AFR AF: 0.0719

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.246

GnomAD4 exome AF: 0.284 AC: 106278 AN: 374182 Hom.: 15605 Cov.: 3 AF XY: 0.281 AC XY: 55197 AN XY: 196424

African (AFR) AF: 0.0733 AC: 554 AN: 7562

American (AMR) AF: 0.232 AC: 2275 AN: 9826

Ashkenazi Jewish (ASJ) AF: 0.309 AC: 3639 AN: 11760

East Asian (EAS) AF: 0.261 AC: 6213 AN: 23762

South Asian (SAS) AF: 0.233 AC: 8115 AN: 34770

European-Finnish (FIN) AF: 0.331 AC: 9440 AN: 28544

Middle Eastern (MID) AF: 0.278 AC: 494 AN: 1776

European-Non Finnish (NFE) AF: 0.297 AC: 69344 AN: 233636

Other (OTH) AF: 0.275 AC: 6204 AN: 22546

GnomAD4 genome AF: 0.226 AC: 34340 AN: 152152 Hom.: 4710 Cov.: 32 AF XY: 0.228 AC XY: 16958 AN XY: 74364

African (AFR) AF: 0.0718 AC: 2983 AN: 41554

American (AMR) AF: 0.240 AC: 3665 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.315 AC: 1092 AN: 3470

East Asian (EAS) AF: 0.239 AC: 1228 AN: 5148

South Asian (SAS) AF: 0.224 AC: 1077 AN: 4816

European-Finnish (FIN) AF: 0.337 AC: 3567 AN: 10590

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.292 AC: 19820 AN: 67962

Other (OTH) AF: 0.245 AC: 517 AN: 2114

Alfa AF: 0.242 Hom.: 1020

Bravo AF: 0.210

Asia WGS AF: 0.251 AC: 873 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	3.3
DANN	Benign	0.56
PhyloP100		-1.6
PromoterAI		-0.062	Neutral
Mutation Taster		=300/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.53		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.53		Position offset: 2

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

Other links and lift over

dbSNP: rs3809717; hg19: chr17-37886986;