rs1570209

Variant names:

• chr20-37400428-T-A
• rs1570209
• NM_198291.3:c.1039+134T>A

Your query was ambiguous. Multiple possible variants found:

• chr20-37400428-T-A
• chr20-37400428-T-C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_198291.3(SRC):​c.1039+134T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SRC NM_198291.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.84
• Publications: 4 publications found

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]

SRC Gene-Disease associations (from GenCC):

• thrombocytopenia 6

  Inheritance: AD Classification: MODERATE, SUPPORTIVE, LIMITED Submitted by: ClinGen, Orphanet, Labcorp Genetics (formerly Invitae)
• colorectal cancer

  Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SRC	NM_198291.3	c.1039+134T>A		intron_variant	Intron 10 of 13	ENST00000373578.7	NP_938033.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SRC	ENST00000373578.7	c.1039+134T>A		intron_variant	Intron 10 of 13	5	NM_198291.3	ENSP00000362680.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 608210 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 306308

African (AFR) AF: 0.00 AC: 0 AN: 13962

American (AMR) AF: 0.00 AC: 0 AN: 13924

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 13208

East Asian (EAS) AF: 0.00 AC: 0 AN: 26808

South Asian (SAS) AF: 0.00 AC: 0 AN: 36698

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 25940

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2150

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 446072

Other (OTH) AF: 0.00 AC: 0 AN: 29448

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 3023

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.27
DANN	Benign	0.26
PhyloP100		-3.8

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.17		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1570209; hg19: chr20-36028831;