XM_011535654.3:c.-286-16022T>A

Variant names:

• chr6-116076619-A-T
• rs12527159
• XM_011535654.3:c.-286-16022T>A

Variant summary

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

The XM_011535654.3(FRK):​c.-286-16022T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 152,130 control chromosomes in the GnomAD database, including 2,892 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 0.18 (2892 hom., cov: 33)
• Consequence: FRK XM_011535654.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.391

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FRK	XM_011535654.3	c.-286-16022T>A		intron_variant	Intron 1 of 8		XP_011533956.1
FRK	XM_011535655.3	c.-283-16025T>A		intron_variant	Intron 1 of 8		XP_011533957.1
FRK	XM_011535656.3	c.5+23873T>A		intron_variant	Intron 1 of 7		XP_011533958.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289376	ENST00000692859.2	n.222+23873T>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27117 AN: 152014 Hom.: 2887 Cov.: 33

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.0395

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.178 AC: 27152 AN: 152130 Hom.: 2892 Cov.: 33 AF XY: 0.180 AC XY: 13396 AN XY: 74350

Gnomad4 AFR AF: 0.291

Gnomad4 AMR AF: 0.202

Gnomad4 ASJ AF: 0.189

Gnomad4 EAS AF: 0.0396

Gnomad4 SAS AF: 0.190

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.116

Gnomad4 OTH AF: 0.163

Alfa AF: 0.153 Hom.: 256

Bravo AF: 0.188

Asia WGS AF: 0.143 AC: 496 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.6
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12527159; hg19: chr6-116397782; COSMIC: COSV60271292;