6-115987881-T-C

Position:

• chr6-115987881-T-C

Variant summary

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

The NM_002031.3(FRK):​c.466+15996A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.649 in 151,928 control chromosomes in the GnomAD database, including 32,510 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 0.65 (32510 hom., cov: 32)
• Consequence: FRK NM_002031.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44

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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.81 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FRK	NM_002031.3	c.466+15996A>G		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+15996A>G		intron_variant		1	NM_002031.3	ENSP00000476145	P1
	ENST00000692859.2	n.223-85703A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.649 AC: 98519 AN: 151810 Hom.: 32484 Cov.: 32

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.671

Gnomad AMR AF: 0.768

Gnomad ASJ AF: 0.737

Gnomad EAS AF: 0.831

Gnomad SAS AF: 0.742

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.674

Gnomad OTH AF: 0.685

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

GnomAD4 genome AF: 0.649 AC: 98595 AN: 151928 Hom.: 32510 Cov.: 32 AF XY: 0.649 AC XY: 48167 AN XY: 74250

Gnomad4 AFR AF: 0.535

Gnomad4 AMR AF: 0.768

Gnomad4 ASJ AF: 0.737

Gnomad4 EAS AF: 0.831

Gnomad4 SAS AF: 0.742

Gnomad4 FIN AF: 0.592

Gnomad4 NFE AF: 0.674

Gnomad4 OTH AF: 0.683

Alfa AF: 0.683 Hom.: 22665

Bravo AF: 0.661

Asia WGS AF: 0.728 AC: 2535 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.46
DANN	Benign	0.45

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: rs1933739; hg19: chr6-116309044; COSMIC: COSV73384218;