chr10-63624807-A-G

Position:

• chr10-63624807-A-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
REEP3	NM_001001330.3	c.*3938A>G		3_prime_UTR_variant	8/8	ENST00000373758.5
LOC105378329	XR_001747467.3	n.295+12T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
REEP3	ENST00000373758.5	c.*3938A>G		3_prime_UTR_variant	8/8	1	NM_001001330.3	P1

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

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

Gnomad4 AFR AF: 0.431

Gnomad4 AMR AF: 0.595

Gnomad4 ASJ AF: 0.580

Gnomad4 EAS AF: 0.543

Gnomad4 SAS AF: 0.603

Gnomad4 FIN AF: 0.581

Gnomad4 NFE AF: 0.551

Gnomad4 OTH AF: 0.556

Alfa AF: 0.548 Hom.: 27729

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

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: rs7089698; hg19: chr10-65384567;