rs7171755

Positions:

• chr15-73558239-G-A

Variant summary

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

The NM_001042367.2(REC114):​c.637-1513G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.451 in 151,950 control chromosomes in the GnomAD database, including 15,714 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 0.45 (15714 hom., cov: 32)
• Consequence: REC114 NM_001042367.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.238

Genes affected

REC114 (HGNC:25065): (REC114 meiotic recombination protein) The protein encoded by this gene is orthologous to the mouse meiotic recombination protein REC114, which is involved in DNA double-strand break formation during meiosis. The encoded protein is conserved in most eukaryotes and was first discovered and characterized in yeast. [provided by RefSeq, Feb 2017]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.503 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
REC114	NM_001042367.2	c.637-1513G>A		intron_variant		ENST00000331090.11	NP_001035826.1
REC114	NM_001348772.2	c.553-1513G>A		intron_variant			NP_001335701.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
REC114	ENST00000331090.11	c.637-1513G>A		intron_variant		1	NM_001042367.2	ENSP00000328423	P1
REC114	ENST00000560581.1	c.553-1513G>A		intron_variant		2		ENSP00000452908

Frequencies

GnomAD3 genomes AF: 0.451 AC: 68407 AN: 151834 Hom.: 15675 Cov.: 32

Gnomad AFR AF: 0.502

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.461

Gnomad EAS AF: 0.518

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.417

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.451 AC: 68512 AN: 151950 Hom.: 15714 Cov.: 32 AF XY: 0.452 AC XY: 33593 AN XY: 74256

Gnomad4 AFR AF: 0.502

Gnomad4 AMR AF: 0.502

Gnomad4 ASJ AF: 0.461

Gnomad4 EAS AF: 0.519

Gnomad4 SAS AF: 0.421

Gnomad4 FIN AF: 0.417

Gnomad4 NFE AF: 0.408

Gnomad4 OTH AF: 0.454

Alfa AF: 0.424 Hom.: 11894

Bravo AF: 0.461

Asia WGS AF: 0.462 AC: 1609 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.3
DANN	Benign	0.51

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: rs7171755; hg19: chr15-73850580;