rs7248982

Variant names:

• chr19-13886580-C-A
• rs7248982
• NM_001345843.2:c.1669-525G>T

Your query was ambiguous. Multiple possible variants found:

• chr19-13886580-C-A
• chr19-13886580-C-G
• chr19-13886580-C-T

Variant summary

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

The NM_001345843.2(BRME1):​c.1669-525G>T 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 152,032 control chromosomes in the GnomAD database, including 11,991 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 (11991 hom., cov: 32)
• Consequence: BRME1 NM_001345843.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.713
• 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=-0.93).
• 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 rank	MANE	Protein	UniProt
BRME1	NM_001345843.2	c.1669-525G>T		intron_variant	Intron 6 of 8	ENST00000586783.6	NP_001332772.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BRME1	ENST00000586783.6	c.1669-525G>T		intron_variant	Intron 6 of 8	5	NM_001345843.2	ENSP00000465822.1

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51768 AN: 151914 Hom.: 11951 Cov.: 32

Gnomad AFR AF: 0.661

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.294

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.341 AC: 51860 AN: 152032 Hom.: 11991 Cov.: 32 AF XY: 0.335 AC XY: 24894 AN XY: 74308

African (AFR) AF: 0.662 AC: 27419 AN: 41430

American (AMR) AF: 0.255 AC: 3898 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 486 AN: 3468

East Asian (EAS) AF: 0.293 AC: 1511 AN: 5158

South Asian (SAS) AF: 0.286 AC: 1384 AN: 4832

European-Finnish (FIN) AF: 0.165 AC: 1752 AN: 10592

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

European-Non Finnish (NFE) AF: 0.216 AC: 14652 AN: 67974

Other (OTH) AF: 0.288 AC: 608 AN: 2110

Alfa AF: 0.224 Hom.: 2195

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	-0.93
CADD	Benign	0.47
DANN	Benign	0.80
PhyloP100		-0.71
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: rs7248982; hg19: chr19-13997393;