rs8111004

Variant names:

• chr19-13901352-A-G
• rs8111004
• NM_001345843.2:c.31+3510T>C

Variant summary

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

The NM_001345843.2(BRME1):​c.31+3510T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 151,866 control chromosomes in the GnomAD database, including 11,950 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 0.34 (11950 hom., cov: 30)
• Consequence: BRME1 NM_001345843.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.179
• Publications: 3 publications found

Genes affected

BRME1 (HGNC:28153): (break repair meiotic recombinase recruitment factor 1) Predicted to be involved in meiosis I and spermatogenesis. Predicted to be located in chromosome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.655 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001345843.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BRME1	NM_001345843.2	MANE Select	c.31+3510T>C		intron	N/A	NP_001332772.2
	BRME1	NM_001393645.1		c.31+3510T>C		intron	N/A	NP_001380574.1
	BRME1	NM_001393646.1		c.31+3510T>C		intron	N/A	NP_001380575.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BRME1	ENST00000586783.6	TSL:5 MANE Select	c.31+3510T>C		intron	N/A	ENSP00000465822.1
	BRME1	ENST00000346736.6	TSL:2	c.31+3510T>C		intron	N/A	ENSP00000254336.1
	BRME1	ENST00000591586.5	TSL:5	c.31+3510T>C		intron	N/A	ENSP00000466723.1

Frequencies

GnomAD3 genomes AF: 0.340 AC: 51654 AN: 151748 Hom.: 11910 Cov.: 30

Gnomad AFR AF: 0.661

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.341 AC: 51746 AN: 151866 Hom.: 11950 Cov.: 30 AF XY: 0.335 AC XY: 24837 AN XY: 74250

African (AFR) AF: 0.662 AC: 27361 AN: 41358

American (AMR) AF: 0.255 AC: 3877 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 485 AN: 3468

East Asian (EAS) AF: 0.295 AC: 1524 AN: 5170

South Asian (SAS) AF: 0.285 AC: 1374 AN: 4816

European-Finnish (FIN) AF: 0.166 AC: 1752 AN: 10576

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.215 AC: 14616 AN: 67950

Other (OTH) AF: 0.289 AC: 607 AN: 2102

Alfa AF: 0.305 Hom.: 1534

Bravo AF: 0.362

Asia WGS AF: 0.354 AC: 1230 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.64
PhyloP100		-0.18
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: rs8111004; hg19: chr19-14012165;