rs10778292

Variant names:

• chr12-103866509-T-C
• rs10778292
• ENST00000548520.2:n.2101A>G

Variant summary

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

The ENST00000548520.2(ENSG00000293399):​n.2101A>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: ENSG00000293399 ENST00000548520.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.77
• Publications: 7 publications found

Genes affected

ENSG00000293399 (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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
TTC41P	NR_027249.1	n.3142A>G		non_coding_transcript_exon_variant	Exon 11 of 16

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293399	ENST00000548520.2	n.2101A>G		non_coding_transcript_exon_variant	Exon 6 of 10	5
ENSG00000293399	ENST00000548527.5	n.240A>G		non_coding_transcript_exon_variant	Exon 3 of 7	5
TTC41P	ENST00000551270.1	n.2596A>G		non_coding_transcript_exon_variant	Exon 10 of 15	6

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

GnomAD2 exomes AF: 0.146 AC: 20299 AN: 139154 AF XY: 0.151

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 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

African (AFR) AF: 0.257 AC: 2214 AN: 8600

American (AMR) AF: 0.0786 AC: 2141 AN: 27232

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 1799 AN: 10744

East Asian (EAS) AF: 0.0432 AC: 393 AN: 9100

South Asian (SAS) AF: 0.217 AC: 12937 AN: 59524

European-Finnish (FIN) AF: 0.193 AC: 2466 AN: 12772

Middle Eastern (MID) AF: 0.105 AC: 291 AN: 2772

European-Non Finnish (NFE) AF: 0.140 AC: 21951 AN: 156738

Other (OTH) AF: 0.149 AC: 2105 AN: 14140

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

African (AFR) AF: 0.257 AC: 10643 AN: 41452

American (AMR) AF: 0.111 AC: 1693 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 607 AN: 3466

East Asian (EAS) AF: 0.0392 AC: 203 AN: 5176

South Asian (SAS) AF: 0.216 AC: 1041 AN: 4814

European-Finnish (FIN) AF: 0.198 AC: 2096 AN: 10570

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.140 AC: 9523 AN: 67992

Other (OTH) AF: 0.165 AC: 348 AN: 2114

Alfa AF: 0.148 Hom.: 3356

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
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs10778292; hg19: chr12-104260287;