NM_002398.3:c.889-16653A>G

Variant names:

• chr2-66531290-A-G
• rs6710341
• NM_002398.3:c.889-16653A>G

Variant summary

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

The NM_002398.3(MEIS1):​c.889-16653A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 152,162 control chromosomes in the GnomAD database, including 2,138 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 0.16 (2138 hom., cov: 32)
• Consequence: MEIS1 NM_002398.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0120
• Publications: 19 publications found

Genes affected

MEIS1 (HGNC:7000): (Meis homeobox 1) Homeobox genes, of which the most well-characterized category is represented by the HOX genes, play a crucial role in normal development. In addition, several homeoproteins are involved in neoplasia. This gene encodes a homeobox protein belonging to the TALE ('three amino acid loop extension') family of homeodomain-containing proteins. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MEIS1	NM_002398.3	c.889-16653A>G		intron_variant	Intron 8 of 12	ENST00000272369.14	NP_002389.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MEIS1	ENST00000272369.14	c.889-16653A>G		intron_variant	Intron 8 of 12	1	NM_002398.3	ENSP00000272369.8

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24750 AN: 152042 Hom.: 2141 Cov.: 32

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.163 AC: 24756 AN: 152162 Hom.: 2138 Cov.: 32 AF XY: 0.165 AC XY: 12267 AN XY: 74390

African (AFR) AF: 0.162 AC: 6729 AN: 41480

American (AMR) AF: 0.156 AC: 2389 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.145 AC: 503 AN: 3472

East Asian (EAS) AF: 0.277 AC: 1434 AN: 5176

South Asian (SAS) AF: 0.296 AC: 1428 AN: 4822

European-Finnish (FIN) AF: 0.145 AC: 1540 AN: 10604

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.149 AC: 10156 AN: 68006

Other (OTH) AF: 0.164 AC: 347 AN: 2114

Alfa AF: 0.158 Hom.: 5412

Bravo AF: 0.163

Asia WGS AF: 0.244 AC: 848 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.9
DANN	Benign	0.59
PhyloP100		0.012
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs6710341; hg19: chr2-66758422;