chrX-34943403-CTCCCGAGACTCCGGTGTCCCGTCTCCGTCCTCAGCT-C

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PM4

The NM_152631.3(FAM47B):​c.577_612delGAGACTCCGGTGTCCCGTCTCCGTCCTCAGCTTCCC​(p.Glu193_Pro204del) variant causes a conservative inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000496 in 1,208,649 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.0000091 ( 0 hom., 0 hem., cov: 22)
Exomes 𝑓: 0.0000046 ( 0 hom. 1 hem. )

Consequence

FAM47B
NM_152631.3 conservative_inframe_deletion

Scores

Not classified

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.70
Variant links:
Genes affected
FAM47B (HGNC:26659): (family with sequence similarity 47 member B)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 4 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PM4
Nonframeshift variant in NON repetitive region in NM_152631.3.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FAM47BNM_152631.3 linkc.577_612delGAGACTCCGGTGTCCCGTCTCCGTCCTCAGCTTCCC p.Glu193_Pro204del conservative_inframe_deletion Exon 1 of 1 ENST00000329357.6 NP_689844.2 Q8NA70

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FAM47BENST00000329357.6 linkc.577_612delGAGACTCCGGTGTCCCGTCTCCGTCCTCAGCTTCCC p.Glu193_Pro204del conservative_inframe_deletion Exon 1 of 1 6 NM_152631.3 ENSP00000328307.5 Q8NA70

Frequencies

GnomAD3 genomes
AF:
0.00000906
AC:
1
AN:
110409
Hom.:
0
Cov.:
22
AF XY:
0.00
AC XY:
0
AN XY:
32637
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000190
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.00000455
AC:
5
AN:
1098240
Hom.:
0
AF XY:
0.00000275
AC XY:
1
AN XY:
363594
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000594
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.00000906
AC:
1
AN:
110409
Hom.:
0
Cov.:
22
AF XY:
0.00
AC XY:
0
AN XY:
32637
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000190
Gnomad4 OTH
AF:
0.00

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Uncertain:1
Sep 03, 2021
Revvity Omics, Revvity
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1926810807; hg19: chrX-34961520; API