ENST00000397829.9:n.636G>A

Variant names:

• chr6-167376672-C-T
• rs200905775
• ENST00000397829.9:n.636G>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP6_Moderate

The ENST00000397829.9(TCP10L3):​n.636G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0018 (0 hom., cov: 9)
  • Exomes 𝑓: 0.0030 (2 hom.)
  • Failed GnomAD Quality Control
• Consequence: TCP10L3 ENST00000397829.9 non_coding_transcript_exon
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.51
• Publications: 1 publications found

Genes affected

TCP10L3 (HGNC:):

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

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• BP6: Variant 6-167376672-C-T is Benign according to our data. Variant chr6-167376672-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 769701.Status of the report is criteria_provided_single_submitter, 1 stars.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TCP10L3	NR_163193.1		n.516G>A		non_coding_transcript_exon	Exon 3 of 6
	TCP10L3	NR_163194.1		n.662G>A		non_coding_transcript_exon	Exon 5 of 8
	TCP10L3	NR_163195.1		n.589G>A		non_coding_transcript_exon	Exon 4 of 7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TCP10L3	ENST00000397829.9	TSL:1	n.636G>A		non_coding_transcript_exon	Exon 5 of 8
	TCP10L3	ENST00000460930.2	TSL:1	n.438G>A		non_coding_transcript_exon	Exon 3 of 3
	TCP10L3	ENST00000366827.6	TSL:5	n.662G>A		non_coding_transcript_exon	Exon 5 of 9

Frequencies

GnomAD3 genomes AF: 0.00174 AC: 129 AN: 74168 Hom.: 0 Cov.: 9

Gnomad AFR AF: 0.00102

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00911

Gnomad ASJ AF: 0.000582

Gnomad EAS AF: 0.00899

Gnomad SAS AF: 0.00428

Gnomad FIN AF: 0.000227

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000409

Gnomad OTH AF: 0.00746

GnomAD2 exomes AF: 0.00422 AC: 396 AN: 93760 AF XY: 0.00406

Gnomad AFR exome AF: 0.00187

Gnomad AMR exome AF: 0.0150

Gnomad ASJ exome AF: 0.000840

Gnomad EAS exome AF: 0.0163

Gnomad FIN exome AF: 0.000213

Gnomad NFE exome AF: 0.00130

Gnomad OTH exome AF: 0.00639

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00299 AC: 2471 AN: 826396 Hom.: 2 Cov.: 12 AF XY: 0.00319 AC XY: 1330 AN XY: 416298

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

African (AFR) AF: 0.00192 AC: 40 AN: 20850

American (AMR) AF: 0.0272 AC: 558 AN: 20500

Ashkenazi Jewish (ASJ) AF: 0.000957 AC: 15 AN: 15678

East Asian (EAS) AF: 0.0197 AC: 503 AN: 25550

South Asian (SAS) AF: 0.00668 AC: 356 AN: 53306

European-Finnish (FIN) AF: 0.00166 AC: 56 AN: 33662

Middle Eastern (MID) AF: 0.000595 AC: 2 AN: 3362

European-Non Finnish (NFE) AF: 0.00134 AC: 827 AN: 617008

Other (OTH) AF: 0.00313 AC: 114 AN: 36480

⚠️ 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 Data not reliable, filtered out with message: AS_VQSR AF: 0.00177 AC: 131 AN: 74206 Hom.: 0 Cov.: 9 AF XY: 0.00188 AC XY: 65 AN XY: 34624

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

African (AFR) AF: 0.00107 AC: 21 AN: 19610

American (AMR) AF: 0.00911 AC: 53 AN: 5818

Ashkenazi Jewish (ASJ) AF: 0.000582 AC: 1 AN: 1718

East Asian (EAS) AF: 0.00901 AC: 25 AN: 2774

South Asian (SAS) AF: 0.00429 AC: 7 AN: 1632

European-Finnish (FIN) AF: 0.000227 AC: 1 AN: 4406

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 176

European-Non Finnish (NFE) AF: 0.000409 AC: 15 AN: 36714

Other (OTH) AF: 0.00849 AC: 8 AN: 942

⚠️ 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: 0.00464 Hom.: 0

ClinVar

ClinVar submissions as Germline

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.19
DANN	Benign	0.50
PhyloP100		-1.5

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.24		Details are displayed if max score is > 0.2
DS_AL_spliceai		0.24		Position offset: 32

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

Other links and lift over

dbSNP: rs200905775; hg19: chr6-167790160; COSMIC: COSV64751205; COSMIC: COSV64751205;