rs210937

Variant names:

• chr6-135219242-G-A
• rs210937
• XR_001744368.2:n.177-3742C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-135219242-G-A
• chr6-135219242-G-C
• chr6-135219242-G-T

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.140
• Publications: 7 publications found

Genes affected

LOC105378011 (HGNC:):

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]

ACMG classification

Our verdict: Benign. The variant received -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	c.*1262G>A		downstream_gene_variant		ENST00000341911.10	NP_001123645.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.601 AC: 91357 AN: 152016 Hom.: 30061 Cov.: 33

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

African (AFR) AF: 0.871 AC: 1089 AN: 1250

American (AMR) AF: 0.425 AC: 360 AN: 848

Ashkenazi Jewish (ASJ) AF: 0.373 AC: 833 AN: 2234

East Asian (EAS) AF: 0.451 AC: 2925 AN: 6480

South Asian (SAS) AF: 0.546 AC: 154 AN: 282

European-Finnish (FIN) AF: 0.593 AC: 262 AN: 442

Middle Eastern (MID) AF: 0.421 AC: 90 AN: 214

European-Non Finnish (NFE) AF: 0.492 AC: 9926 AN: 20160

Other (OTH) AF: 0.488 AC: 1372 AN: 2812

GnomAD4 genome AF: 0.601 AC: 91481 AN: 152134 Hom.: 30120 Cov.: 33 AF XY: 0.600 AC XY: 44622 AN XY: 74352

African (AFR) AF: 0.882 AC: 36650 AN: 41536

American (AMR) AF: 0.437 AC: 6676 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.377 AC: 1308 AN: 3470

East Asian (EAS) AF: 0.503 AC: 2605 AN: 5180

South Asian (SAS) AF: 0.506 AC: 2441 AN: 4824

European-Finnish (FIN) AF: 0.577 AC: 6083 AN: 10538

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.504 AC: 34236 AN: 67992

Other (OTH) AF: 0.526 AC: 1111 AN: 2112

Alfa AF: 0.528 Hom.: 65809

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
PhyloP100		-0.14
Mutation Taster		=100/0	polymorphism

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs210937; hg19: chr6-135540380; COSMIC: COSV57197014;