chr14-95641618-C-T

Variant names:

• chr14-95641618-C-T
• rs7148498
• ENST00000555032.2:n.317-123C>T

Variant summary

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

The ENST00000555032.2(TCL6):​n.317-123C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 152,176 control chromosomes in the GnomAD database, including 1,207 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 0.12 (1206 hom., cov: 32)
  • Exomes 𝑓: 0.11 (1 hom.)
• Consequence: TCL6 ENST00000555032.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0590
• Publications: 9 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.179 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000555032.2. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TCL6	ENST00000555032.2	TSL:4	n.317-123C>T		intron	N/A
	TCL6	ENST00000655483.1		n.103-123C>T		intron	N/A
	TCL6	ENST00000661620.1		n.188-123C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17805 AN: 152040 Hom.: 1202 Cov.: 32

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.0926

Gnomad ASJ AF: 0.0988

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.0858

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.0859

Gnomad OTH AF: 0.129

GnomAD4 exome AF: 0.111 AC: 2 AN: 18 Hom.: 1 AF XY: 0.00 AC XY: 0 AN XY: 14

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.200 AC: 2 AN: 10

Other (OTH) AF: 0.00 AC: 0 AN: 4

GnomAD4 genome AF: 0.117 AC: 17828 AN: 152158 Hom.: 1206 Cov.: 32 AF XY: 0.117 AC XY: 8685 AN XY: 74396

African (AFR) AF: 0.183 AC: 7575 AN: 41472

American (AMR) AF: 0.0926 AC: 1415 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0988 AC: 343 AN: 3472

East Asian (EAS) AF: 0.106 AC: 550 AN: 5178

South Asian (SAS) AF: 0.175 AC: 842 AN: 4824

European-Finnish (FIN) AF: 0.0858 AC: 910 AN: 10606

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.0859 AC: 5842 AN: 68006

Other (OTH) AF: 0.128 AC: 271 AN: 2110

Alfa AF: 0.0904 Hom.: 1189

Bravo AF: 0.119

Asia WGS AF: 0.126 AC: 437 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.6
DANN	Benign	0.77
PhyloP100		-0.059
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs7148498; hg19: chr14-96107955;