rs9400883

Variant names:

• chr6-115984950-A-G
• rs9400883
• NM_002031.3:c.467-16211T>C

Your query was ambiguous. Multiple possible variants found:

• chr6-115984950-A-G
• chr6-115984950-A-T

Variant summary

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

The NM_002031.3(FRK):​c.467-16211T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0969 in 152,152 control chromosomes in the GnomAD database, including 1,035 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 0.097 (1035 hom., cov: 31)
• Consequence: FRK NM_002031.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.556
• Publications: 6 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.305 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FRK	NM_002031.3	c.467-16211T>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.467-16211T>C		intron_variant	Intron 2 of 7	1	NM_002031.3	ENSP00000476145.1
ENSG00000289376	ENST00000692859.3	n.269-82772T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0969 AC: 14737 AN: 152034 Hom.: 1032 Cov.: 31

Gnomad AFR AF: 0.0222

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.0763

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.0956

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

GnomAD4 genome AF: 0.0969 AC: 14741 AN: 152152 Hom.: 1035 Cov.: 31 AF XY: 0.0990 AC XY: 7364 AN XY: 74360

African (AFR) AF: 0.0221 AC: 918 AN: 41558

American (AMR) AF: 0.135 AC: 2066 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 356 AN: 3470

East Asian (EAS) AF: 0.318 AC: 1637 AN: 5148

South Asian (SAS) AF: 0.217 AC: 1045 AN: 4812

European-Finnish (FIN) AF: 0.0763 AC: 809 AN: 10606

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7617 AN: 67972

Other (OTH) AF: 0.0970 AC: 205 AN: 2114

Alfa AF: 0.114 Hom.: 2244

Bravo AF: 0.0974

Asia WGS AF: 0.228 AC: 794 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.1
DANN	Benign	0.80
PhyloP100		-0.56
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: rs9400883; hg19: chr6-116306113;