NM_001001330.3:c.105+10983T>C

Variant names:

• chr10-63577393-T-C
• rs10822184
• NM_001001330.3:c.105+10983T>C

Variant summary

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

The NM_001001330.3(REEP3):​c.105+10983T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.48 in 151,930 control chromosomes in the GnomAD database, including 17,869 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 0.48 (17869 hom., cov: 30)
• Consequence: REEP3 NM_001001330.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.358
• Publications: 43 publications found

Genes affected

REEP3 (HGNC:23711): (receptor accessory protein 3) Predicted to enable microtubule binding activity. Involved in mitotic nuclear membrane reassembly. Predicted to be integral component of membrane. Predicted to be active in cytoplasmic microtubule; endoplasmic reticulum membrane; and endoplasmic reticulum tubular network. [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=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.554 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001001330.3. 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
	REEP3	NM_001001330.3	MANE Select	c.105+10983T>C		intron	N/A	NP_001001330.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	REEP3	ENST00000373758.5	TSL:1 MANE Select	c.105+10983T>C		intron	N/A	ENSP00000362863.4

Frequencies

GnomAD3 genomes AF: 0.481 AC: 72970 AN: 151812 Hom.: 17866 Cov.: 30

Gnomad AFR AF: 0.404

Gnomad AMI AF: 0.661

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.573

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.508

Gnomad OTH AF: 0.503

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

GnomAD4 genome AF: 0.480 AC: 72977 AN: 151930 Hom.: 17869 Cov.: 30 AF XY: 0.480 AC XY: 35652 AN XY: 74242

African (AFR) AF: 0.404 AC: 16723 AN: 41436

American (AMR) AF: 0.514 AC: 7844 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.622 AC: 2157 AN: 3470

East Asian (EAS) AF: 0.422 AC: 2167 AN: 5138

South Asian (SAS) AF: 0.572 AC: 2749 AN: 4810

European-Finnish (FIN) AF: 0.476 AC: 5026 AN: 10552

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.508 AC: 34500 AN: 67948

Other (OTH) AF: 0.505 AC: 1065 AN: 2108

Alfa AF: 0.489 Hom.: 29894

Bravo AF: 0.475

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.6
DANN	Benign	0.58
PhyloP100		-0.36
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: rs10822184; hg19: chr10-65337153;