rs8014810

Variant names:

• chr14-35855824-G-T
• rs8014810
• NM_032352.4:c.442-6766G>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
BRMS1L	NM_032352.4	c.442-6766G>T		intron_variant	Intron 4 of 9	ENST00000216807.12	NP_115728.2
BRMS1L	XM_005268128.2	c.442-6766G>T		intron_variant	Intron 4 of 9		XP_005268185.1
BRMS1L	XM_047431806.1	c.298-6766G>T		intron_variant	Intron 6 of 11		XP_047287762.1
BRMS1L	XM_017021705.1	c.298-6766G>T		intron_variant	Intron 4 of 9		XP_016877194.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BRMS1L	ENST00000216807.12	c.442-6766G>T		intron_variant	Intron 4 of 9	1	NM_032352.4	ENSP00000216807.6

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

African (AFR) AF: 0.559 AC: 23154 AN: 41412

American (AMR) AF: 0.234 AC: 3574 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.200 AC: 692 AN: 3466

East Asian (EAS) AF: 0.483 AC: 2496 AN: 5170

South Asian (SAS) AF: 0.260 AC: 1253 AN: 4812

European-Finnish (FIN) AF: 0.189 AC: 1985 AN: 10526

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.181 AC: 12298 AN: 67962

Other (OTH) AF: 0.274 AC: 577 AN: 2106

Alfa AF: 0.227 Hom.: 13350

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
PhyloP100		0.51
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: rs8014810; hg19: chr14-36325030;