6-115994940-C-A

Position:

• chr6-115994940-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002031.3(FRK):​c.466+8937G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.384 in 151,966 control chromosomes in the GnomAD database, including 12,374 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 0.38 (12374 hom., cov: 32)
• Consequence: FRK NM_002031.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36

Genes affected

FRK (HGNC:3955): (fyn related Src family tyrosine kinase) The protein encoded by this gene belongs to the TYR family of protein kinases. This tyrosine kinase is a nuclear protein and may function during G1 and S phase of the cell cycle and suppress growth. [provided by RefSeq, Jul 2008]

ENSG00000289376 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.756 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FRK	NM_002031.3	c.466+8937G>T		intron_variant		ENST00000606080.2	NP_002022.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FRK	ENST00000606080.2	c.466+8937G>T		intron_variant		1	NM_002031.3	ENSP00000476145.1
ENSG00000289376	ENST00000692859.2	n.223-92762G>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.384 AC: 58384 AN: 151848 Hom.: 12370 Cov.: 32

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.661

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.776

Gnomad SAS AF: 0.557

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.384 AC: 58407 AN: 151966 Hom.: 12374 Cov.: 32 AF XY: 0.390 AC XY: 28954 AN XY: 74264

Gnomad4 AFR AF: 0.224

Gnomad4 AMR AF: 0.432

Gnomad4 ASJ AF: 0.351

Gnomad4 EAS AF: 0.776

Gnomad4 SAS AF: 0.556

Gnomad4 FIN AF: 0.425

Gnomad4 NFE AF: 0.421

Gnomad4 OTH AF: 0.392

Alfa AF: 0.321 Hom.: 1326

Bravo AF: 0.376

Asia WGS AF: 0.568 AC: 1979 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.033
DANN	Benign	0.53

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

Other links and lift over

dbSNP: rs3822856; hg19: chr6-116316103;