rs11153594

Variant names:

• chr6-116033428-C-T
• rs11153594
• NM_002031.3:c.344+26540G>A

Variant summary

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

The NM_002031.3(FRK):​c.344+26540G>A 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 151,910 control chromosomes in the GnomAD database, including 10,644 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 (10644 hom., cov: 32)
• Consequence: FRK NM_002031.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0180
• Publications: 18 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FRK	NM_002031.3	c.344+26540G>A		intron_variant	Intron 1 of 7	ENST00000606080.2	NP_002022.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FRK	ENST00000606080.2	c.344+26540G>A		intron_variant	Intron 1 of 7	1	NM_002031.3	ENSP00000476145.1
ENSG00000289376	ENST00000692859.3	n.268+67064G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.366 AC: 55566 AN: 151792 Hom.: 10636 Cov.: 32

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.0384

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.401

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: 55603 AN: 151910 Hom.: 10644 Cov.: 32 AF XY: 0.362 AC XY: 26844 AN XY: 74248

African (AFR) AF: 0.333 AC: 13793 AN: 41434

American (AMR) AF: 0.419 AC: 6394 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.448 AC: 1556 AN: 3470

East Asian (EAS) AF: 0.0385 AC: 199 AN: 5172

South Asian (SAS) AF: 0.214 AC: 1033 AN: 4824

European-Finnish (FIN) AF: 0.400 AC: 4218 AN: 10556

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.401 AC: 27234 AN: 67898

Other (OTH) AF: 0.396 AC: 832 AN: 2102

Alfa AF: 0.376 Hom.: 2068

Bravo AF: 0.374

Asia WGS AF: 0.156 AC: 543 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.0
DANN	Benign	0.32
PhyloP100		0.018
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11153594; hg19: chr6-116354591;