chr9-2130917-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_003070.5(SMARCA2):​c.3981+6980G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 152,092 control chromosomes in the GnomAD database, including 3,066 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 0.17 ( 3066 hom., cov: 32)

Consequence

SMARCA2
NM_003070.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.66
Variant links:
Genes affected
SMARCA2 (HGNC:11098): (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2) The protein encoded by this gene is a member of the SWI/SNF family of proteins and is highly 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. Alternatively spliced transcript variants encoding different isoforms have been found for this gene, which contains a trinucleotide repeat (CAG) length polymorphism. [provided by RefSeq, Jan 2014]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SMARCA2NM_003070.5 linkuse as main transcriptc.3981+6980G>A intron_variant ENST00000349721.8
SMARCA2NM_001289396.1 linkuse as main transcriptc.3981+6980G>A intron_variant
SMARCA2NM_001289397.2 linkuse as main transcriptc.3807+6980G>A intron_variant
SMARCA2NM_139045.4 linkuse as main transcriptc.3981+6980G>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SMARCA2ENST00000349721.8 linkuse as main transcriptc.3981+6980G>A intron_variant 5 NM_003070.5 P2P51531-1

Frequencies

GnomAD3 genomes
AF:
0.172
AC:
26135
AN:
151976
Hom.:
3063
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.295
Gnomad AMI
AF:
0.0735
Gnomad AMR
AF:
0.146
Gnomad ASJ
AF:
0.102
Gnomad EAS
AF:
0.436
Gnomad SAS
AF:
0.213
Gnomad FIN
AF:
0.0883
Gnomad MID
AF:
0.0918
Gnomad NFE
AF:
0.0988
Gnomad OTH
AF:
0.155
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.172
AC:
26174
AN:
152092
Hom.:
3066
Cov.:
32
AF XY:
0.174
AC XY:
12907
AN XY:
74384
show subpopulations
Gnomad4 AFR
AF:
0.295
Gnomad4 AMR
AF:
0.146
Gnomad4 ASJ
AF:
0.102
Gnomad4 EAS
AF:
0.436
Gnomad4 SAS
AF:
0.213
Gnomad4 FIN
AF:
0.0883
Gnomad4 NFE
AF:
0.0988
Gnomad4 OTH
AF:
0.157
Alfa
AF:
0.0886
Hom.:
211
Bravo
AF:
0.182
Asia WGS
AF:
0.287
AC:
1002
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.053
DANN
Benign
0.47

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: rs6475522; hg19: chr9-2130917; API