19-13901352-A-G

Position:

• chr19-13901352-A-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BRME1	NM_001345843.2	c.31+3510T>C		intron_variant		ENST00000586783.6	NP_001332772.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BRME1	ENST00000586783.6	c.31+3510T>C		intron_variant		5	NM_001345843.2	ENSP00000465822	P1
BRME1	ENST00000346736.6	c.31+3510T>C		intron_variant		2		ENSP00000254336
BRME1	ENST00000585755.1	c.31+3510T>C		intron_variant		3		ENSP00000466119
BRME1	ENST00000591586.5	c.31+3510T>C		intron_variant		5		ENSP00000466723

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

Gnomad4 AFR AF: 0.662

Gnomad4 AMR AF: 0.255

Gnomad4 ASJ AF: 0.140

Gnomad4 EAS AF: 0.295

Gnomad4 SAS AF: 0.285

Gnomad4 FIN AF: 0.166

Gnomad4 NFE AF: 0.215

Gnomad4 OTH AF: 0.289

Alfa AF: 0.294 Hom.: 1376

Bravo AF: 0.362

Asia WGS AF: 0.354 AC: 1230 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.64

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: rs8111004; hg19: chr19-14012165;