rs10778292

Positions:

• chr12-103866509-T-C

Variant summary

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

The NR_027249.1(TTC41P):​n.3142A>G 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 0.16 in 453,684 control chromosomes in the GnomAD database, including 6,639 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 0.17 (2636 hom., cov: 32)
  • Exomes 𝑓: 0.15 (4003 hom.)
• Consequence: TTC41P NR_027249.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.77

Genes affected

(HGNC:):

TTC41P (HGNC:49210): (tetratricopeptide repeat domain 41, pseudogene) Predicted to be located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TTC41P	NR_027249.1	n.3142A>G		non_coding_transcript_exon_variant	11/16

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000548520.2	n.2101A>G		non_coding_transcript_exon_variant	6/10	5
TTC41P	ENST00000551270.1	n.2596A>G		non_coding_transcript_exon_variant	10/15
	ENST00000548527.5	n.240A>G		non_coding_transcript_exon_variant	3/7	5
	ENST00000552065.2	n.1358A>G		non_coding_transcript_exon_variant	6/12	3

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26371 AN: 151944 Hom.: 2631 Cov.: 32

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.0387

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.166

GnomAD3 exomes AF: 0.146 AC: 20299 AN: 139154 Hom.: 1770 AF XY: 0.151 AC XY: 11423 AN XY: 75420

Gnomad AFR exome AF: 0.263

Gnomad AMR exome AF: 0.0795

Gnomad ASJ exome AF: 0.171

Gnomad EAS exome AF: 0.0418

Gnomad SAS exome AF: 0.219

Gnomad FIN exome AF: 0.197

Gnomad NFE exome AF: 0.142

Gnomad OTH exome AF: 0.137

GnomAD4 exome AF: 0.153 AC: 46297 AN: 301622 Hom.: 4003 Cov.: 0 AF XY: 0.159 AC XY: 27198 AN XY: 171354

Gnomad4 AFR exome AF: 0.257

Gnomad4 AMR exome AF: 0.0786

Gnomad4 ASJ exome AF: 0.167

Gnomad4 EAS exome AF: 0.0432

Gnomad4 SAS exome AF: 0.217

Gnomad4 FIN exome AF: 0.193

Gnomad4 NFE exome AF: 0.140

Gnomad4 OTH exome AF: 0.149

GnomAD4 genome AF: 0.174 AC: 26409 AN: 152062 Hom.: 2636 Cov.: 32 AF XY: 0.175 AC XY: 13022 AN XY: 74330

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.175

Gnomad4 EAS AF: 0.0392

Gnomad4 SAS AF: 0.216

Gnomad4 FIN AF: 0.198

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.165

Alfa AF: 0.146 Hom.: 2373

Bravo AF: 0.170

Asia WGS AF: 0.137 AC: 474 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.028
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10778292; hg19: chr12-104260287;