Variant 14-44504951-A-AGGGGCCTCCTCAGCTGGTGGAGGCTGAACTTCAGAG details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 4P and 2B. PM2PM4BP6_Moderate

The NM_032135.4(FSCB):c.2036_2037insCTCTGAAGTTCAGCCTCCACCAGCTGAGGAGGCCCC(p.Pro679_Ala680insSerGluValGlnProProProAlaGluGluAlaPro) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: not found (cov: 32)

Consequence

FSCB
NM_032135.4 disruptive_inframe_insertion

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0700

Variant links:

Genes affected

FSCB (HGNC:20494): (fibrous sheath CABYR binding protein) Predicted to enable calcium ion binding activity. Predicted to be involved in negative regulation of protein sumoylation. Predicted to be active in sperm fibrous sheath and sperm principal piece. [provided by Alliance of Genome Resources, Apr 2022]

FSCB links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

PM4

Nonframeshift variant in NON repetitive region in NM_032135.4.

BP6

Variant 14-44504951-A-AGGGGCCTCCTCAGCTGGTGGAGGCTGAACTTCAGAG is Benign according to our data. Variant chr14-44504951-A-AGGGGCCTCCTCAGCTGGTGGAGGCTGAACTTCAGAG is described in ClinVar as [Benign]. Clinvar id is 768650.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FSCB	NM_032135.4 link	c.2036_2037insCTCTGAAGTTCAGCCTCCACCAGCTGAGGAGGCCCC	p.Pro679_Ala680insSerGluValGlnProProProAlaGluGluAlaPro	disruptive_inframe_insertion	1/1	ENST00000340446.5	NP_115511.3	Q5H9T9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FSCB	ENST00000340446.5 link	c.2036_2037insCTCTGAAGTTCAGCCTCCACCAGCTGAGGAGGCCCC	p.Pro679_Ala680insSerGluValGlnProProProAlaGluGluAlaPro	disruptive_inframe_insertion	1/1	6	NM_032135.4	ENSP00000344579.4		Q5H9T9

Frequencies

GnomAD3 genomes

Cov.:

GnomAD3 exomes

AF:

0.000129

AC:

AN:

185850

Hom.:

AF XY:

0.000120

AC XY:

AN XY:

99780

show subpopulations

Gnomad AFR exome

AF:

0.0000771

Gnomad AMR exome

AF:

0.000111

Gnomad ASJ exome

AF:

0.000495

Gnomad EAS exome

AF:

0.000123

Gnomad SAS exome

AF:

0.000201

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000105

Gnomad OTH exome

AF:

0.000453

GnomAD4 exome

Cov.:

GnomAD4 genome

Cov.:

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Dec 31, 2019

- -

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over