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GeneBe

rs7953508

chr12-93589778-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The XM_011538935.2(SOCS2):c.591+14605C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 152,106 control chromosomes in the GnomAD database, including 8,312 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 ( 8312 hom., cov: 33)

Consequence

SOCS2
XM_011538935.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.587
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.45).
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.453 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SOCS2XM_011538935.2 linkuse as main transcriptc.591+14605C>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.319
AC:
48449
AN:
151986
Hom.:
8290
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.459
Gnomad AMI
AF:
0.321
Gnomad AMR
AF:
0.304
Gnomad ASJ
AF:
0.183
Gnomad EAS
AF:
0.338
Gnomad SAS
AF:
0.193
Gnomad FIN
AF:
0.265
Gnomad MID
AF:
0.149
Gnomad NFE
AF:
0.261
Gnomad OTH
AF:
0.290
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.319
AC:
48521
AN:
152106
Hom.:
8312
Cov.:
33
AF XY:
0.315
AC XY:
23400
AN XY:
74356
show subpopulations
Gnomad4 AFR
AF:
0.459
Gnomad4 AMR
AF:
0.304
Gnomad4 ASJ
AF:
0.183
Gnomad4 EAS
AF:
0.338
Gnomad4 SAS
AF:
0.193
Gnomad4 FIN
AF:
0.265
Gnomad4 NFE
AF:
0.261
Gnomad4 OTH
AF:
0.291
Alfa
AF:
0.266
Hom.:
11256
Bravo
AF:
0.330
Asia WGS
AF:
0.268
AC:
936
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.45
Cadd
Benign
15
Dann
Benign
0.55

Splicing

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: rs7953508; hg19: chr12-93983554; API