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GeneBe

rs210948

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001130173.2(MYB):c.2170-7202T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.536 in 152,162 control chromosomes in the GnomAD database, including 22,263 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 0.54 ( 22263 hom., cov: 33)

Consequence

MYB
NM_001130173.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.361
Variant links:
Genes affected
MYB (HGNC:7545): (MYB proto-oncogene, transcription factor) This gene encodes a protein with three HTH DNA-binding domains that functions as a transcription regulator. This protein plays an essential role in the regulation of hematopoiesis. This gene may be aberrently expressed or rearranged or undergo translocation in leukemias and lymphomas, and is considered to be an oncogene. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.664 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MYBNM_001130173.2 linkuse as main transcriptc.2170-7202T>C intron_variant ENST00000341911.10
LOC105378011XR_001744368.2 linkuse as main transcriptn.278+4737A>G intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MYBENST00000341911.10 linkuse as main transcriptc.2170-7202T>C intron_variant 1 NM_001130173.2 A1P10242-4

Frequencies

GnomAD3 genomes
AF:
0.535
AC:
81419
AN:
152044
Hom.:
22243
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.671
Gnomad AMI
AF:
0.343
Gnomad AMR
AF:
0.519
Gnomad ASJ
AF:
0.438
Gnomad EAS
AF:
0.501
Gnomad SAS
AF:
0.491
Gnomad FIN
AF:
0.468
Gnomad MID
AF:
0.402
Gnomad NFE
AF:
0.482
Gnomad OTH
AF:
0.521
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.536
AC:
81496
AN:
152162
Hom.:
22263
Cov.:
33
AF XY:
0.533
AC XY:
39655
AN XY:
74392
show subpopulations
Gnomad4 AFR
AF:
0.670
Gnomad4 AMR
AF:
0.520
Gnomad4 ASJ
AF:
0.438
Gnomad4 EAS
AF:
0.501
Gnomad4 SAS
AF:
0.491
Gnomad4 FIN
AF:
0.468
Gnomad4 NFE
AF:
0.482
Gnomad4 OTH
AF:
0.522
Alfa
AF:
0.524
Hom.:
2568
Bravo
AF:
0.545
Asia WGS
AF:
0.530
AC:
1843
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
Cadd
Benign
7.0
Dann
Benign
0.73

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs210948; hg19: chr6-135531800; API