rs797045979

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PM4_Supporting

The NM_003072.5(SMARCA4):​c.2893_2895delATC​(p.Ile965del) variant causes a conservative inframe deletion change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 33)

Consequence

SMARCA4
NM_003072.5 conservative_inframe_deletion

Scores

Not classified

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 9.10
Variant links:
Genes affected
SMARCA4 (HGNC:11100): (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4) The protein encoded by this gene is a member of the SWI/SNF family of proteins and is similar to the brahma protein of Drosophila. Members of this family have helicase and ATPase activities and are thought to regulate transcription of certain genes by altering the chromatin structure around those genes. The encoded protein is part of the large ATP-dependent chromatin remodeling complex SNF/SWI, which is required for transcriptional activation of genes normally repressed by chromatin. In addition, this protein can bind BRCA1, as well as regulate the expression of the tumorigenic protein CD44. Mutations in this gene cause rhabdoid tumor predisposition syndrome type 2. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2012]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 3 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PM4
Nonframeshift variant in NON repetitive region in NM_003072.5. Strenght limited to Supporting due to length of the change: 1aa.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SMARCA4NM_001387283.1 linkuse as main transcriptc.2893_2895delATC p.Ile965del conservative_inframe_deletion 20/36 ENST00000646693.2 NP_001374212.1
SMARCA4NM_003072.5 linkuse as main transcriptc.2893_2895delATC p.Ile965del conservative_inframe_deletion 20/35 ENST00000344626.10 NP_003063.2 P51532-1A7E2E1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SMARCA4ENST00000646693.2 linkuse as main transcriptc.2893_2895delATC p.Ile965del conservative_inframe_deletion 20/36 NM_001387283.1 ENSP00000495368.1 Q9HBD4
SMARCA4ENST00000344626.10 linkuse as main transcriptc.2893_2895delATC p.Ile965del conservative_inframe_deletion 20/351 NM_003072.5 ENSP00000343896.4 P51532-1
SMARCA4ENST00000643549.1 linkuse as main transcriptc.2893_2895delATC p.Ile965del conservative_inframe_deletion 20/35 ENSP00000493975.1 A0A2R8Y4P4
SMARCA4ENST00000541122.6 linkuse as main transcriptc.2893_2895delATC p.Ile965del conservative_inframe_deletion 21/355 ENSP00000445036.2 P51532-4
SMARCA4ENST00000643296.1 linkuse as main transcriptc.2893_2895delATC p.Ile965del conservative_inframe_deletion 20/34 ENSP00000496635.1 P51532-4
SMARCA4ENST00000644737.1 linkuse as main transcriptc.2893_2895delATC p.Ile965del conservative_inframe_deletion 20/34 ENSP00000495548.1 P51532-4
SMARCA4ENST00000589677.5 linkuse as main transcriptc.2893_2895delATC p.Ile965del conservative_inframe_deletion 21/355 ENSP00000464778.1 P51532-3
SMARCA4ENST00000643995.1 linkuse as main transcriptc.2305_2307delATC p.Ile769del conservative_inframe_deletion 17/32 ENSP00000496004.1 A0A2R8YGG3
SMARCA4ENST00000644963.1 linkuse as main transcriptc.1537_1539delATC p.Ile513del conservative_inframe_deletion 13/28 ENSP00000495599.1 A0A2R8YG32
SMARCA4ENST00000644065.1 linkuse as main transcriptc.1618_1620delATC p.Ile540del conservative_inframe_deletion 13/27 ENSP00000493615.1 A0A2R8Y440
SMARCA4ENST00000642350.1 linkuse as main transcriptc.1378_1380delATC p.Ile460del conservative_inframe_deletion 12/27 ENSP00000495355.1 A0A2R8Y6N0
SMARCA4ENST00000643857.1 linkuse as main transcriptc.1246_1248delATC p.Ile416del conservative_inframe_deletion 11/25 ENSP00000494159.1 A0A2R8Y526

Frequencies

GnomAD3 genomes
Cov.:
33
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Cov.:
33

ClinVar

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

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingGenetic Services Laboratory, University of ChicagoApr 10, 2014- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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

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

Other links and lift over

dbSNP: rs797045979; hg19: chr19-11134221; API