10-63624807-A-G

Variant names:

• chr10-63624807-A-G
• rs7089698
• NM_001001330.3:c.*3938A>G

Variant summary

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

The NM_001001330.3(REEP3):​c.*3938A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.528 in 151,946 control chromosomes in the GnomAD database, including 21,501 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 0.53 (21501 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: REEP3 NM_001001330.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.41
• Publications: 9 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]

LOC105378329 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.585 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
REEP3	NM_001001330.3	c.*3938A>G		3_prime_UTR_variant	Exon 8 of 8	ENST00000373758.5	NP_001001330.1
LOC105378329	XR_001747467.3	n.295+12T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
REEP3	ENST00000373758.5	c.*3938A>G		3_prime_UTR_variant	Exon 8 of 8	1	NM_001001330.3	ENSP00000362863.4

Frequencies

GnomAD3 genomes AF: 0.528 AC: 80164 AN: 151828 Hom.: 21497 Cov.: 32

Gnomad AFR AF: 0.431

Gnomad AMI AF: 0.699

Gnomad AMR AF: 0.595

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.545

Gnomad SAS AF: 0.603

Gnomad FIN AF: 0.581

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.555

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.528 AC: 80182 AN: 151946 Hom.: 21501 Cov.: 32 AF XY: 0.531 AC XY: 39443 AN XY: 74262

African (AFR) AF: 0.431 AC: 17861 AN: 41464

American (AMR) AF: 0.595 AC: 9090 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.580 AC: 2013 AN: 3468

East Asian (EAS) AF: 0.543 AC: 2807 AN: 5166

South Asian (SAS) AF: 0.603 AC: 2903 AN: 4818

European-Finnish (FIN) AF: 0.581 AC: 6141 AN: 10568

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.551 AC: 37415 AN: 67882

Other (OTH) AF: 0.556 AC: 1170 AN: 2106

Alfa AF: 0.539 Hom.: 39627

Bravo AF: 0.522

Asia WGS AF: 0.536 AC: 1863 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.8
DANN	Benign	0.65
PhyloP100		1.4
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: rs7089698; hg19: chr10-65384567;