6-116065971-C-T

Variant names:

• chr6-116065971-C-T
• rs1999930
• XM_011535654.3:c.-286-5374G>A

Variant summary

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

The ENST00000692859.3(ENSG00000289376):​n.268+34521G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 152,172 control chromosomes in the GnomAD database, including 3,822 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 0.20 (3822 hom., cov: 32)
• Consequence: ENSG00000289376 ENST00000692859.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.98
• Publications: 43 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=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000692859.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289376	ENST00000692859.3		n.268+34521G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29804 AN: 152054 Hom.: 3822 Cov.: 32

Gnomad AFR AF: 0.0622

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.00385

Gnomad SAS AF: 0.0675

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.196 AC: 29811 AN: 152172 Hom.: 3822 Cov.: 32 AF XY: 0.190 AC XY: 14120 AN XY: 74382

African (AFR) AF: 0.0623 AC: 2590 AN: 41544

American (AMR) AF: 0.220 AC: 3359 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.281 AC: 975 AN: 3464

East Asian (EAS) AF: 0.00386 AC: 20 AN: 5188

South Asian (SAS) AF: 0.0679 AC: 328 AN: 4828

European-Finnish (FIN) AF: 0.222 AC: 2350 AN: 10574

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.285 AC: 19400 AN: 67976

Other (OTH) AF: 0.242 AC: 511 AN: 2114

Alfa AF: 0.248 Hom.: 16951

Bravo AF: 0.194

Asia WGS AF: 0.0500 AC: 174 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.85
DANN	Benign	0.66
PhyloP100		-2.0

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1999930;

hg19: chr6-116387134;

COSMIC: COSV50466933;