16-11379799-T-C

Variant summary

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

The NM_001370704.1(LOC400499):​c.9958+3843A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 152,142 control chromosomes in the GnomAD database, including 8,049 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 0.32 ( 8049 hom., cov: 33)

Consequence

LOC400499
NM_001370704.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.664
Variant links:
Genes affected
RMI2 (HGNC:28349): (RecQ mediated genome instability 2) RMI2 is a component of the BLM (RECQL3; MIM 604610) complex, which plays a role in homologous recombination-dependent DNA repair and is essential for genome stability (Xu et al., 2008 [PubMed 18923082]).[supplied by OMIM, Nov 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.353 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LOC400499NM_001370704.1 linkuse as main transcriptc.9958+3843A>G intron_variant ENST00000696174.1 NP_001357633.1
LOC105371082XR_933070.4 linkuse as main transcriptn.179-23T>C intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ENST00000696174.1 linkuse as main transcriptc.9958+3843A>G intron_variant NM_001370704.1 ENSP00000512464 A2

Frequencies

GnomAD3 genomes
AF:
0.322
AC:
48946
AN:
152024
Hom.:
8050
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.288
Gnomad AMI
AF:
0.317
Gnomad AMR
AF:
0.276
Gnomad ASJ
AF:
0.369
Gnomad EAS
AF:
0.288
Gnomad SAS
AF:
0.334
Gnomad FIN
AF:
0.294
Gnomad MID
AF:
0.313
Gnomad NFE
AF:
0.357
Gnomad OTH
AF:
0.326
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.322
AC:
48969
AN:
152142
Hom.:
8049
Cov.:
33
AF XY:
0.317
AC XY:
23581
AN XY:
74378
show subpopulations
Gnomad4 AFR
AF:
0.288
Gnomad4 AMR
AF:
0.276
Gnomad4 ASJ
AF:
0.369
Gnomad4 EAS
AF:
0.288
Gnomad4 SAS
AF:
0.333
Gnomad4 FIN
AF:
0.294
Gnomad4 NFE
AF:
0.357
Gnomad4 OTH
AF:
0.326
Alfa
AF:
0.347
Hom.:
19081
Bravo
AF:
0.318
Asia WGS
AF:
0.276
AC:
960
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
2.0
DANN
Benign
0.31

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: rs7203055; hg19: chr16-11473656; API