rs11635553

chr15-73457267-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.159+13923G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0251 in 152,140 control chromosomes in the GnomAD database, including 95 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 0.025 (95 hom., cov: 31)
• Consequence: REC114 NM_001042367.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.495

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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0578 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
REC114	NM_001042367.2	c.159+13923G>A		intron_variant		ENST00000331090.11
REC114	NM_001348772.2	c.159+13923G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
REC114	ENST00000331090.11	c.159+13923G>A		intron_variant		1	NM_001042367.2	P1
REC114	ENST00000560581.1	c.159+13923G>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.0250 AC: 3804 AN: 152022 Hom.: 95 Cov.: 31

Gnomad AFR AF: 0.0596

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0146

Gnomad ASJ AF: 0.0135

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.00725

Gnomad FIN AF: 0.00349

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0138

Gnomad OTH AF: 0.0196

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

GnomAD4 genome AF: 0.0251 AC: 3819 AN: 152140 Hom.: 95 Cov.: 31 AF XY: 0.0243 AC XY: 1807 AN XY: 74382

Gnomad4 AFR AF: 0.0598

Gnomad4 AMR AF: 0.0145

Gnomad4 ASJ AF: 0.0135

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.00725

Gnomad4 FIN AF: 0.00349

Gnomad4 NFE AF: 0.0139

Gnomad4 OTH AF: 0.0194

Alfa AF: 0.0155 Hom.: 25

Bravo AF: 0.0272

Asia WGS AF: 0.00693 AC: 24 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	2.3
Dann	Benign	0.79

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: rs11635553; hg19: chr15-73749608;