chr2-66529281-A-G

Variant names:

• chr2-66529281-A-G
• rs11677371
• NM_002398.3:c.888+16987A>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.888+16987A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.606 in 151,900 control chromosomes in the GnomAD database, including 28,392 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 0.61 (28392 hom., cov: 31)
• Consequence: MEIS1 NM_002398.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.817
• Publications: 4 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=-0.47).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.789 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002398.3. 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
	MEIS1	NM_002398.3	MANE Select	c.888+16987A>G		intron	N/A	NP_002389.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MEIS1	ENST00000272369.14	TSL:1 MANE Select	c.888+16987A>G		intron	N/A	ENSP00000272369.8
	MEIS1	ENST00000488550.5	TSL:1	c.888+16987A>G		intron	N/A	ENSP00000475161.1
	MEIS1	ENST00000398506.6	TSL:5	c.882+16987A>G		intron	N/A	ENSP00000381518.2

Frequencies

GnomAD3 genomes AF: 0.606 AC: 92042 AN: 151782 Hom.: 28376 Cov.: 31

Gnomad AFR AF: 0.530

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.679

Gnomad ASJ AF: 0.697

Gnomad EAS AF: 0.809

Gnomad SAS AF: 0.793

Gnomad FIN AF: 0.595

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.603

Gnomad OTH AF: 0.641

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

GnomAD4 genome AF: 0.606 AC: 92094 AN: 151900 Hom.: 28392 Cov.: 31 AF XY: 0.614 AC XY: 45556 AN XY: 74238

African (AFR) AF: 0.530 AC: 21915 AN: 41358

American (AMR) AF: 0.679 AC: 10382 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.697 AC: 2416 AN: 3468

East Asian (EAS) AF: 0.810 AC: 4185 AN: 5168

South Asian (SAS) AF: 0.794 AC: 3814 AN: 4806

European-Finnish (FIN) AF: 0.595 AC: 6265 AN: 10536

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.603 AC: 40966 AN: 67970

Other (OTH) AF: 0.644 AC: 1357 AN: 2108

Alfa AF: 0.606 Hom.: 5887

Bravo AF: 0.611

Asia WGS AF: 0.766 AC: 2664 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
CADD	Benign	8.2
DANN	Benign	0.93
PhyloP100		0.82
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: rs11677371; hg19: chr2-66756413;