rs8015016

Positions:

• chr14-95656071-A-G
• chr14-95656071-A-T

Variant summary

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

The NR_028288.2(TCL6):​n.361+1445A>G variant causes a intron, non coding transcript 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 NR_028288.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TCL6	NR_028288.2	n.361+1445A>G		intron_variant, non_coding_transcript_variant
TCL6	NR_152604.1	n.361+1445A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TCL6	ENST00000459662.5	n.1280+1445A>G		intron_variant, non_coding_transcript_variant		2
TCL6	ENST00000357168.6	n.945+1445A>G		intron_variant, non_coding_transcript_variant		2
TCL6	ENST00000483087.5	n.1280+1445A>G		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.222

Gnomad4 AMR AF: 0.354

Gnomad4 ASJ AF: 0.193

Gnomad4 EAS AF: 0.229

Gnomad4 SAS AF: 0.303

Gnomad4 FIN AF: 0.129

Gnomad4 NFE AF: 0.195

Gnomad4 OTH AF: 0.231

Alfa AF: 0.202 Hom.: 7417

Bravo AF: 0.236

Asia WGS AF: 0.294 AC: 1024 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8015016; hg19: chr14-96122408;