6-116052368-A-G

Variant names:

• chr6-116052368-A-G
• rs6568920
• NM_002031.3:c.344+7600T>C

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+7600T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.784 in 152,022 control chromosomes in the GnomAD database, including 47,237 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 0.78 (47237 hom., cov: 31)
• Consequence: FRK NM_002031.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0810
• Publications: 4 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 = 0.85 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002031.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FRK	NM_002031.3	MANE Select	c.344+7600T>C		intron	N/A	NP_002022.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FRK	ENST00000606080.2	TSL:1 MANE Select	c.344+7600T>C		intron	N/A	ENSP00000476145.1
	ENSG00000289376	ENST00000692859.3		n.268+48124T>C		intron	N/A
	ENSG00000287933	ENST00000848837.1		n.360-9531A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.785 AC: 119169 AN: 151904 Hom.: 47214 Cov.: 31

Gnomad AFR AF: 0.665

Gnomad AMI AF: 0.879

Gnomad AMR AF: 0.862

Gnomad ASJ AF: 0.821

Gnomad EAS AF: 0.817

Gnomad SAS AF: 0.814

Gnomad FIN AF: 0.825

Gnomad MID AF: 0.915

Gnomad NFE AF: 0.824

Gnomad OTH AF: 0.820

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

GnomAD4 genome AF: 0.784 AC: 119247 AN: 152022 Hom.: 47237 Cov.: 31 AF XY: 0.784 AC XY: 58291 AN XY: 74314

African (AFR) AF: 0.665 AC: 27587 AN: 41460

American (AMR) AF: 0.862 AC: 13152 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.821 AC: 2848 AN: 3468

East Asian (EAS) AF: 0.817 AC: 4228 AN: 5176

South Asian (SAS) AF: 0.813 AC: 3915 AN: 4814

European-Finnish (FIN) AF: 0.825 AC: 8720 AN: 10574

Middle Eastern (MID) AF: 0.912 AC: 268 AN: 294

European-Non Finnish (NFE) AF: 0.824 AC: 55997 AN: 67952

Other (OTH) AF: 0.818 AC: 1730 AN: 2116

Alfa AF: 0.814 Hom.: 25450

Bravo AF: 0.786

Asia WGS AF: 0.765 AC: 2660 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.6
DANN	Benign	0.78
PhyloP100		-0.081
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: rs6568920; hg19: chr6-116373531; COSMIC: COSV74177014;