NM_001042367.2:c.159+13923G>A

Variant names:

• chr15-73457267-G-A
• rs11635553
• NM_001042367.2:c.159+13923G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
REC114	NM_001042367.2	c.159+13923G>A		intron_variant	Intron 1 of 5	ENST00000331090.11	NP_001035826.1
REC114	NM_001348772.2	c.159+13923G>A		intron_variant	Intron 1 of 4		NP_001335701.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
REC114	ENST00000331090.11	c.159+13923G>A		intron_variant	Intron 1 of 5	1	NM_001042367.2	ENSP00000328423.6
REC114	ENST00000560581.1	c.159+13923G>A		intron_variant	Intron 1 of 4	2		ENSP00000452908.1

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

African (AFR) AF: 0.0598 AC: 2480 AN: 41474

American (AMR) AF: 0.0145 AC: 222 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0135 AC: 47 AN: 3470

East Asian (EAS) AF: 0.00154 AC: 8 AN: 5188

South Asian (SAS) AF: 0.00725 AC: 35 AN: 4826

European-Finnish (FIN) AF: 0.00349 AC: 37 AN: 10590

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0139 AC: 942 AN: 67992

Other (OTH) AF: 0.0194 AC: 41 AN: 2112

Alfa AF: 0.0208 Hom.: 81

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
PhyloP100		-0.49
Mutation Taster		=100/0	polymorphism

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: rs11635553; hg19: chr15-73749608;