rs12106024

Variant summary

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

The NM_198291.3(SRC):​c.-247+4690C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 152,104 control chromosomes in the GnomAD database, including 4,385 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 0.23 ( 4385 hom., cov: 32)

Consequence

SRC
NM_198291.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.48
Variant links:
Genes affected
SRC (HGNC:11283): (SRC proto-oncogene, non-receptor tyrosine kinase) This gene is highly similar to the v-src gene of Rous sarcoma virus. This proto-oncogene may play a role in the regulation of embryonic development and cell growth. The protein encoded by this gene is a tyrosine-protein kinase whose activity can be inhibited by phosphorylation by c-SRC kinase. Mutations in this gene could be involved in the malignant progression of colon cancer. Two transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 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=-0.85).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SRCNM_198291.3 linkuse as main transcriptc.-247+4690C>G intron_variant ENST00000373578.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SRCENST00000373578.7 linkuse as main transcriptc.-247+4690C>G intron_variant 5 NM_198291.3 P1P12931-1

Frequencies

GnomAD3 genomes
AF:
0.235
AC:
35662
AN:
151986
Hom.:
4374
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.259
Gnomad AMI
AF:
0.229
Gnomad AMR
AF:
0.178
Gnomad ASJ
AF:
0.248
Gnomad EAS
AF:
0.187
Gnomad SAS
AF:
0.219
Gnomad FIN
AF:
0.142
Gnomad MID
AF:
0.288
Gnomad NFE
AF:
0.251
Gnomad OTH
AF:
0.234
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.235
AC:
35707
AN:
152104
Hom.:
4385
Cov.:
32
AF XY:
0.228
AC XY:
16964
AN XY:
74356
show subpopulations
Gnomad4 AFR
AF:
0.260
Gnomad4 AMR
AF:
0.178
Gnomad4 ASJ
AF:
0.248
Gnomad4 EAS
AF:
0.187
Gnomad4 SAS
AF:
0.220
Gnomad4 FIN
AF:
0.142
Gnomad4 NFE
AF:
0.251
Gnomad4 OTH
AF:
0.239
Alfa
AF:
0.100
Hom.:
156
Bravo
AF:
0.237
Asia WGS
AF:
0.222
AC:
776
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
1.8
DANN
Benign
0.22

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: rs12106024; hg19: chr20-35979348; API