X-139588447-TA-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate

The NM_001171876.2(MCF2):c.2599-10del variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.0000092 (0 hom., 0 hem., cov: 22)
  • Exomes 𝑓: 0.00058 (0 hom. 2 hem.)
  • Failed GnomAD Quality Control
• Consequence: MCF2 NM_001171876.2 splice_polypyrimidine_tract, intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.784

Genes affected

MCF2 (HGNC:6940): (MCF.2 cell line derived transforming sequence) The oncogenic protein encoded by this gene is a guanine nucleotide exchange factor (GEF) that exerts control over some members of the Rho family of small GTPases. Several transcript variants encoding different isoforms have been found for this gene. These isoforms exhibit different expression patterns and varying levels of GEF activity.[provided by RefSeq, Jan 2010]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• BP6: Variant X-139588447-TA-T is Benign according to our data. Variant chrX-139588447-TA-T is described in ClinVar as [Benign]. Clinvar id is 771945.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MCF2	NM_001171876.2	c.2599-10del		splice_polypyrimidine_tract_variant, intron_variant		ENST00000519895.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MCF2	ENST00000519895.6	c.2599-10del		splice_polypyrimidine_tract_variant, intron_variant		2	NM_001171876.2	P4

Frequencies

GnomAD3 genomes AF: 0.00 AC: 1 AN: 108138 Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0 AN XY: 31096 FAILED QC

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: 0.000185

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.000584 AC: 573 AN: 981259 Hom.: 0 Cov.: 20 AF XY: 0.00000711 AC XY: 2 AN XY: 281347

Gnomad4 AFR exome AF: 0.000887

Gnomad4 AMR exome AF: 0.000655

Gnomad4 ASJ exome AF: 0.000337

Gnomad4 EAS exome AF: 0.000385

Gnomad4 SAS exome AF: 0.000333

Gnomad4 FIN exome AF: 0.000128

Gnomad4 NFE exome AF: 0.000634

Gnomad4 OTH exome AF: 0.000433

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000925 AC: 1 AN: 108138 Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0 AN XY: 31096

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: 0.000185

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

Alfa AF: 0.00565 Hom.: 0

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Aug 16, 2017

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs758334892; hg19: chrX-138670606;