rs1544155

Positions:

• chr6-116025231-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.345-21233G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.366 in 151,940 control chromosomes in the GnomAD database, including 10,634 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 0.37 (10634 hom., cov: 31)
• Consequence: FRK NM_002031.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.655

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FRK	NM_002031.3	c.345-21233G>T		intron_variant		ENST00000606080.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FRK	ENST00000606080.2	c.345-21233G>T		intron_variant		1	NM_002031.3	P1
	ENST00000692859.2	n.222+75261G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.366 AC: 55569 AN: 151822 Hom.: 10627 Cov.: 31

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.449

Gnomad EAS AF: 0.0387

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.400

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

GnomAD4 genome AF: 0.366 AC: 55605 AN: 151940 Hom.: 10634 Cov.: 31 AF XY: 0.362 AC XY: 26855 AN XY: 74274

Gnomad4 AFR AF: 0.333

Gnomad4 AMR AF: 0.420

Gnomad4 ASJ AF: 0.449

Gnomad4 EAS AF: 0.0388

Gnomad4 SAS AF: 0.215

Gnomad4 FIN AF: 0.401

Gnomad4 NFE AF: 0.400

Gnomad4 OTH AF: 0.396

Alfa AF: 0.381 Hom.: 5325

Bravo AF: 0.374

Asia WGS AF: 0.157 AC: 545 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.44
DANN	Benign	0.65

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: rs1544155; hg19: chr6-116346394; COSMIC: COSV74177010;