14-95656071-A-G

Variant names:

• chr14-95656071-A-G
• rs8015016
• ENST00000357168.6:n.945+1445A>G

Variant summary

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

The ENST00000357168.6(TCL6):​n.945+1445A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 152,196 control chromosomes in the GnomAD database, including 3,957 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 0.22 (3957 hom., cov: 33)
• Consequence: TCL6 ENST00000357168.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502
• Publications: 19 publications found

Genes affected

TCL6 (HGNC:13463): (T cell leukemia/lymphoma 6)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.346 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000357168.6. 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
	TCL6	NR_028288.2		n.361+1445A>G		intron	N/A
	TCL6	NR_152604.1		n.361+1445A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TCL6	ENST00000357168.6	TSL:2	n.945+1445A>G		intron	N/A
	TCL6	ENST00000459662.5	TSL:2	n.1280+1445A>G		intron	N/A
	TCL6	ENST00000483087.5	TSL:2	n.1280+1445A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33308 AN: 152078 Hom.: 3951 Cov.: 33

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.219 AC: 33347 AN: 152196 Hom.: 3957 Cov.: 33 AF XY: 0.220 AC XY: 16379 AN XY: 74428

African (AFR) AF: 0.222 AC: 9226 AN: 41536

American (AMR) AF: 0.354 AC: 5407 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 668 AN: 3470

East Asian (EAS) AF: 0.229 AC: 1189 AN: 5188

South Asian (SAS) AF: 0.303 AC: 1463 AN: 4826

European-Finnish (FIN) AF: 0.129 AC: 1369 AN: 10594

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.195 AC: 13267 AN: 67984

Other (OTH) AF: 0.231 AC: 488 AN: 2114

Alfa AF: 0.204 Hom.: 15130

Bravo AF: 0.236

Asia WGS AF: 0.294 AC: 1024 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	7.8
DANN	Benign	0.92
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs8015016; hg19: chr14-96122408;