rs6122566

Variant names:

• chr20-37406204-A-G
• rs6122566
• ENST00000811250.1:n.224-579T>C

Your query was ambiguous. Multiple possible variants found:

• chr20-37406204-A-G
• chr20-37406204-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000811250.1(ENSG00000305480):​n.224-579T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 151,528 control chromosomes in the GnomAD database, including 3,574 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 0.14 (3574 hom., cov: 31)
• Consequence: ENSG00000305480 ENST00000811250.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.401
• Publications: 7 publications found

Genes affected

ENSG00000305480 (HGNC:):

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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SRC	NM_198291.3	c.*2825A>G		downstream_gene_variant		ENST00000373578.7	NP_938033.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SRC	ENST00000373578.7	c.*2825A>G		downstream_gene_variant		5	NM_198291.3	ENSP00000362680.2

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20634 AN: 151408 Hom.: 3559 Cov.: 31

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.00330

Gnomad AMR AF: 0.0632

Gnomad ASJ AF: 0.0294

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.0540

Gnomad FIN AF: 0.0152

Gnomad MID AF: 0.0669

Gnomad NFE AF: 0.0198

Gnomad OTH AF: 0.116

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.136 AC: 20678 AN: 151528 Hom.: 3574 Cov.: 31 AF XY: 0.135 AC XY: 9990 AN XY: 74024

African (AFR) AF: 0.400 AC: 16476 AN: 41228

American (AMR) AF: 0.0631 AC: 962 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.0294 AC: 102 AN: 3466

East Asian (EAS) AF: 0.218 AC: 1118 AN: 5128

South Asian (SAS) AF: 0.0528 AC: 253 AN: 4792

European-Finnish (FIN) AF: 0.0152 AC: 160 AN: 10520

Middle Eastern (MID) AF: 0.0582 AC: 17 AN: 292

European-Non Finnish (NFE) AF: 0.0198 AC: 1345 AN: 67842

Other (OTH) AF: 0.115 AC: 242 AN: 2106

Alfa AF: 0.0584 Hom.: 3107

Bravo AF: 0.152

Asia WGS AF: 0.137 AC: 475 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.39
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs6122566; hg19: chr20-36034607;