NM_002398.3:c.888+16987A>G

Variant names:

• chr2-66529281-A-G
• rs11677371
• NM_002398.3:c.888+16987A>G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MEIS1	NM_002398.3	c.888+16987A>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.888+16987A>G		intron_variant	Intron 8 of 12	1	NM_002398.3	ENSP00000272369.8

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

Gnomad4 AFR AF: 0.530

Gnomad4 AMR AF: 0.679

Gnomad4 ASJ AF: 0.697

Gnomad4 EAS AF: 0.810

Gnomad4 SAS AF: 0.794

Gnomad4 FIN AF: 0.595

Gnomad4 NFE AF: 0.603

Gnomad4 OTH AF: 0.644

Alfa AF: 0.607 Hom.: 5048

Bravo AF: 0.611

Asia WGS AF: 0.766 AC: 2664 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
CADD	Benign	8.2
DANN	Benign	0.93

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

Publications

LitVar

Other links and lift over

dbSNP: rs11677371; hg19: chr2-66756413;