6-116052368-A-G

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.85 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FRK	NM_002031.3	c.344+7600T>C		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+7600T>C		intron_variant	Intron 1 of 7	1	NM_002031.3	ENSP00000476145.1
ENSG00000289376	ENST00000692859.2	n.222+48124T>C		intron_variant	Intron 1 of 1

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

Gnomad4 AFR AF: 0.665

Gnomad4 AMR AF: 0.862

Gnomad4 ASJ AF: 0.821

Gnomad4 EAS AF: 0.817

Gnomad4 SAS AF: 0.813

Gnomad4 FIN AF: 0.825

Gnomad4 NFE AF: 0.824

Gnomad4 OTH AF: 0.818

Alfa AF: 0.812 Hom.: 22802

Bravo AF: 0.786

Asia WGS AF: 0.765 AC: 2660 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.6
DANN	Benign	0.78

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: rs6568920; hg19: chr6-116373531; COSMIC: COSV74177014;