12-39659356-T-G

Variant names:

• chr12-39659356-T-G
• rs10783969
• NM_001031748.4:c.686+9002T>G

Variant summary

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

The NM_001031748.4(REDIC1):​c.686+9002T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.793 in 151,824 control chromosomes in the GnomAD database, including 48,430 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 0.79 (48430 hom., cov: 31)
• Consequence: REDIC1 NM_001031748.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35
• Publications: 2 publications found

Genes affected

REDIC1 (HGNC:26846): (regulator of DNA class I crossover intermediates 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.859 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001031748.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	REDIC1	NM_001031748.4	MANE Select	c.686+9002T>G		intron	N/A	NP_001026918.2
	REDIC1	NM_001319247.2		c.686+9002T>G		intron	N/A	NP_001306176.1
	REDIC1	NR_135051.2		n.701+9002T>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	REDIC1	ENST00000324616.9	TSL:1 MANE Select	c.686+9002T>G		intron	N/A	ENSP00000317671.5
	REDIC1	ENST00000405531.7	TSL:1	c.686+9002T>G		intron	N/A	ENSP00000383897.3
	REDIC1	ENST00000468200.2	TSL:1	n.455+9002T>G		intron	N/A	ENSP00000473371.1

Frequencies

GnomAD3 genomes AF: 0.793 AC: 120264 AN: 151706 Hom.: 48407 Cov.: 31

Gnomad AFR AF: 0.659

Gnomad AMI AF: 0.841

Gnomad AMR AF: 0.809

Gnomad ASJ AF: 0.896

Gnomad EAS AF: 0.626

Gnomad SAS AF: 0.735

Gnomad FIN AF: 0.896

Gnomad MID AF: 0.831

Gnomad NFE AF: 0.865

Gnomad OTH AF: 0.796

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

GnomAD4 genome AF: 0.793 AC: 120345 AN: 151824 Hom.: 48430 Cov.: 31 AF XY: 0.791 AC XY: 58686 AN XY: 74202

African (AFR) AF: 0.659 AC: 27308 AN: 41420

American (AMR) AF: 0.809 AC: 12345 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.896 AC: 3112 AN: 3472

East Asian (EAS) AF: 0.627 AC: 3239 AN: 5168

South Asian (SAS) AF: 0.736 AC: 3540 AN: 4812

European-Finnish (FIN) AF: 0.896 AC: 9383 AN: 10476

Middle Eastern (MID) AF: 0.832 AC: 243 AN: 292

European-Non Finnish (NFE) AF: 0.865 AC: 58734 AN: 67900

Other (OTH) AF: 0.796 AC: 1677 AN: 2108

Alfa AF: 0.772 Hom.: 17061

Bravo AF: 0.784

Asia WGS AF: 0.671 AC: 2330 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.92
DANN	Benign	0.42
PhyloP100		-1.3
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: rs10783969; hg19: chr12-40053158;