6-167373086-A-T

Variant names:

• chr6-167373086-A-T
• rs3798324
• ENST00000397829.9:n.1250T>A

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The ENST00000397829.9(TCP10L3):​n.1250T>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0608 in 1,538,184 control chromosomes in the GnomAD database, including 20 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 0.055 (0 hom., cov: 41)
  • Exomes 𝑓: 0.061 (20 hom.)
• Consequence: TCP10L3 ENST00000397829.9 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.208
• Publications: 1 publications found

Genes affected

TCP10L3 (HGNC:):

TCP10L3 (HGNC:11656): (t-complex 10 like 3 (pseudogene))

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BS2: High Homozygotes in GnomAdExome4 at 20 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000397829.9. 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
	TCP10L3	NR_163193.1		n.*4T>A		downstream_gene	N/A
	TCP10L3	NR_163194.1		n.*4T>A		downstream_gene	N/A
	TCP10L3	NR_163195.1		n.*4T>A		downstream_gene	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TCP10L3	ENST00000397829.9	TSL:1	n.1250T>A		non_coding_transcript_exon	Exon 8 of 8
	TCP10L3	ENST00000463894.7	TSL:2	n.3511T>A		non_coding_transcript_exon	Exon 6 of 6
	TCP10L3	ENST00000617120.5	TSL:5	n.889T>A		non_coding_transcript_exon	Exon 6 of 6

Frequencies

GnomAD3 genomes AF: 0.0552 AC: 8345 AN: 151258 Hom.: 0 Cov.: 41

Gnomad AFR AF: 0.0222

Gnomad AMI AF: 0.0422

Gnomad AMR AF: 0.0833

Gnomad ASJ AF: 0.0838

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.0550

Gnomad MID AF: 0.0255

Gnomad NFE AF: 0.0525

Gnomad OTH AF: 0.0550

GnomAD4 exome AF: 0.0614 AC: 85142 AN: 1386812 Hom.: 20 Cov.: 67 AF XY: 0.0623 AC XY: 42593 AN XY: 684150

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0196 AC: 599 AN: 30504

American (AMR) AF: 0.106 AC: 3255 AN: 30852

Ashkenazi Jewish (ASJ) AF: 0.0938 AC: 2005 AN: 21386

East Asian (EAS) AF: 0.195 AC: 7548 AN: 38694

South Asian (SAS) AF: 0.107 AC: 7808 AN: 73060

European-Finnish (FIN) AF: 0.0614 AC: 3096 AN: 50410

Middle Eastern (MID) AF: 0.0487 AC: 258 AN: 5298

European-Non Finnish (NFE) AF: 0.0524 AC: 56576 AN: 1079640

Other (OTH) AF: 0.0702 AC: 3997 AN: 56968

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.0552 AC: 8362 AN: 151372 Hom.: 0 Cov.: 41 AF XY: 0.0582 AC XY: 4304 AN XY: 73988

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0224 AC: 928 AN: 41484

American (AMR) AF: 0.0837 AC: 1266 AN: 15126

Ashkenazi Jewish (ASJ) AF: 0.0838 AC: 289 AN: 3448

East Asian (EAS) AF: 0.216 AC: 1094 AN: 5076

South Asian (SAS) AF: 0.103 AC: 493 AN: 4766

European-Finnish (FIN) AF: 0.0550 AC: 580 AN: 10542

Middle Eastern (MID) AF: 0.0240 AC: 7 AN: 292

European-Non Finnish (NFE) AF: 0.0525 AC: 3551 AN: 67644

Other (OTH) AF: 0.0554 AC: 116 AN: 2094

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.0523 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.7
DANN	Benign	0.39
PhyloP100		0.21
Mutation Taster		=100/0	polymorphism

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: rs3798324; hg19: chr6-167786574; COSMIC: COSV64752790; COSMIC: COSV64752790;