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GeneBe

rs2282679

Variant summary

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

The NM_000583.4(GC):c.*26-796A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.218 in 152042 control chromosomes in the gnomAD Genomes database, including 4252 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 0.22 ( 4252 hom., cov: 32)

Consequence

GC
NM_000583.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.329

Links

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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=-0.87).
BA1
?
GnomAd highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
GCNM_000583.4 linkuse as main transcriptc.*26-796A>C intron_variant ENST00000273951.13
GCNM_001204306.1 linkuse as main transcriptc.*26-796A>C intron_variant
GCNM_001204307.1 linkuse as main transcriptc.*26-796A>C intron_variant
GCXM_006714177.3 linkuse as main transcriptc.*40-796A>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
GCENST00000273951.13 linkuse as main transcriptc.*26-796A>C intron_variant 1 NM_000583.4 P1P02774-1

Frequencies

GnomAD3 genomes
AF:
0.218
AC:
33097
AN:
152042
Hom.:
4252
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0879
Gnomad AMI
AF:
0.409
Gnomad AMR
AF:
0.222
Gnomad ASJ
AF:
0.288
Gnomad EAS
AF:
0.256
Gnomad SAS
AF:
0.285
Gnomad FIN
AF:
0.186
Gnomad MID
AF:
0.168
Gnomad NFE
AF:
0.287
Gnomad OTH
AF:
0.227
Alfa
AF:
0.275
Hom.:
13557
Bravo
AF:
0.213
Asia WGS
AF:
0.228
AC:
799
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
Cadd
Benign
6.2
Dann
Benign
0.68

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: rs2282679; hg19: chr4-72608383; API