dbSNP rs210937: LOC105378011:n.177-3742C>T (chr6-135219242-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The XR_001744368.2(LOC105378011):n.177-3742C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.581 in 186,856 control chromosomes in the GnomAD database, including 34,391 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 0.60 ( 30120 hom., cov: 33)

Exomes 𝑓: 0.49 ( 4271 hom. )

Consequence

LOC105378011
XR_001744368.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.140

Variant links:

Genes affected

LOC105378011 (HGNC:):

LOC105378011 links:

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]

MYB links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.875 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYB	NM_001130173.2 link	c.*1262G>A		downstream_gene_variant		ENST00000341911.10	NP_001123645.1	P10242-4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYB	ENST00000341911.10 link	c.*1262G>A		downstream_gene_variant		1	NM_001130173.2	ENSP00000339992.5		P10242-4

Frequencies

GnomAD3 genomes

AF:

0.601

AC:

91357

AN:

152016

Hom.:

30061

Cov.:

show subpopulations

Gnomad AFR

AF:

0.882

Gnomad AMI

AF:

0.292

Gnomad AMR

AF:

0.437

Gnomad ASJ

AF:

0.377

Gnomad EAS

AF:

0.503

Gnomad SAS

AF:

0.506

Gnomad FIN

AF:

0.577

Gnomad MID

AF:

0.364

Gnomad NFE

AF:

0.504

Gnomad OTH

AF:

0.520

GnomAD4 exome

AF:

0.490

AC:

17011

AN:

34722

Hom.:

4271

AF XY:

0.491

AC XY:

7889

AN XY:

16054

show subpopulations

Gnomad4 AFR exome

AF:

0.871

Gnomad4 AMR exome

AF:

0.425

Gnomad4 ASJ exome

AF:

0.373

Gnomad4 EAS exome

AF:

0.451

Gnomad4 SAS exome

AF:

0.546

Gnomad4 FIN exome

AF:

0.593

Gnomad4 NFE exome

AF:

0.492

Gnomad4 OTH exome

AF:

0.488

GnomAD4 genome

AF:

0.601

AC:

91481

AN:

152134

Hom.:

30120

Cov.:

AF XY:

0.600

AC XY:

44622

AN XY:

74352

show subpopulations

Gnomad4 AFR

AF:

0.882

Gnomad4 AMR

AF:

0.437

Gnomad4 ASJ

AF:

0.377

Gnomad4 EAS

AF:

0.503

Gnomad4 SAS

AF:

0.506

Gnomad4 FIN

AF:

0.577

Gnomad4 NFE

AF:

0.504

Gnomad4 OTH

AF:

0.526

Alfa

AF:

0.503

Hom.:

33181

Bravo

AF:

0.597

Asia WGS

AF:

0.549

AC:

1908

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

5.5

DANN

Benign

0.67

Splicing

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over