rs210948

Variant names:

• chr6-135210662-T-C
• rs210948
• NM_001130173.2:c.2170-7202T>C

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.361
• Publications: 3 publications found

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]

LOC105378011 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
MYB	NM_001130173.2	c.2170-7202T>C		intron_variant	Intron 15 of 15	ENST00000341911.10	NP_001123645.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYB	ENST00000341911.10	c.2170-7202T>C		intron_variant	Intron 15 of 15	1	NM_001130173.2	ENSP00000339992.5

Frequencies

GnomAD3 genomes AF: 0.535 AC: 81419 AN: 152044 Hom.: 22243 Cov.: 33

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

African (AFR) AF: 0.670 AC: 27835 AN: 41516

American (AMR) AF: 0.520 AC: 7951 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.438 AC: 1519 AN: 3472

East Asian (EAS) AF: 0.501 AC: 2592 AN: 5178

South Asian (SAS) AF: 0.491 AC: 2367 AN: 4824

European-Finnish (FIN) AF: 0.468 AC: 4950 AN: 10568

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.482 AC: 32744 AN: 67986

Other (OTH) AF: 0.522 AC: 1105 AN: 2116

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
PhyloP100		-0.36
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: rs210948; hg19: chr6-135531800;