rs8014810

chr14-35855824-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032352.4(BRMS1L):c.442-6766G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 151,924 control chromosomes in the GnomAD database, including 9,143 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 0.30 (9143 hom., cov: 32)
• Consequence: BRMS1L NM_032352.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.507

Genes affected

BRMS1L (HGNC:20512): (BRMS1 like transcriptional repressor) The protein encoded by this gene shows sequence similarity to the human breast carcinoma metastasis suppressor (BRMS1) protein and the mammalian Sds3 (suppressor of defective silencing 3) proteins. This protein is a component of the mSin3a family of histone deacetylase complexes (HDAC). [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.553 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BRMS1L	NM_032352.4	c.442-6766G>T		intron_variant		ENST00000216807.12
BRMS1L	XM_005268128.2	c.442-6766G>T		intron_variant
BRMS1L	XM_017021705.1	c.298-6766G>T		intron_variant
BRMS1L	XM_047431806.1	c.298-6766G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BRMS1L	ENST00000216807.12	c.442-6766G>T		intron_variant		1	NM_032352.4	P1

Frequencies

GnomAD3 genomes AF: 0.304 AC: 46208 AN: 151806 Hom.: 9116 Cov.: 32

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.194

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.484

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.272

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.305 AC: 46285 AN: 151924 Hom.: 9143 Cov.: 32 AF XY: 0.306 AC XY: 22701 AN XY: 74250

Gnomad4 AFR AF: 0.559

Gnomad4 AMR AF: 0.234

Gnomad4 ASJ AF: 0.200

Gnomad4 EAS AF: 0.483

Gnomad4 SAS AF: 0.260

Gnomad4 FIN AF: 0.189

Gnomad4 NFE AF: 0.181

Gnomad4 OTH AF: 0.274

Alfa AF: 0.203 Hom.: 5882

Bravo AF: 0.317

Asia WGS AF: 0.406 AC: 1413 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	3.7
Dann	Benign	0.61

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: rs8014810; hg19: chr14-36325030;