rs7759033

Variant names:

• chr6-115976351-A-G
• rs7759033
• NM_002031.3:c.467-7612T>C

Your query was ambiguous. Multiple possible variants found:

• chr6-115976351-A-G
• chr6-115976351-A-T

Variant summary

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

The NM_002031.3(FRK):​c.467-7612T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 152,122 control chromosomes in the GnomAD database, including 3,691 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 0.21 (3691 hom., cov: 32)
• Consequence: FRK NM_002031.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.43

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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FRK	NM_002031.3	c.467-7612T>C		intron_variant	Intron 2 of 7	ENST00000606080.2	NP_002022.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FRK	ENST00000606080.2	c.467-7612T>C		intron_variant	Intron 2 of 7	1	NM_002031.3	ENSP00000476145.1
ENSG00000289376	ENST00000692859.2	n.223-74173T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31339 AN: 152006 Hom.: 3684 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.00499

Gnomad SAS AF: 0.0410

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.206 AC: 31370 AN: 152122 Hom.: 3691 Cov.: 32 AF XY: 0.197 AC XY: 14686 AN XY: 74380

Gnomad4 AFR AF: 0.173

Gnomad4 AMR AF: 0.218

Gnomad4 ASJ AF: 0.250

Gnomad4 EAS AF: 0.00520

Gnomad4 SAS AF: 0.0412

Gnomad4 FIN AF: 0.140

Gnomad4 NFE AF: 0.258

Gnomad4 OTH AF: 0.253

Alfa AF: 0.232 Hom.: 2271

Bravo AF: 0.214

Asia WGS AF: 0.0440 AC: 158 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	15
DANN	Benign	0.77

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: rs7759033; hg19: chr6-116297514;