rs11111839

Variant names:

• chr12-103916945-C-A
• rs11111839
• ENST00000388789.5:n.273-862G>T

Variant summary

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

The ENST00000388789.5(ENSG00000293399):​n.273-862G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.08 in 152,180 control chromosomes in the GnomAD database, including 642 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 0.080 (642 hom., cov: 32)
• Consequence: ENSG00000293399 ENST00000388789.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.623
• Publications: 5 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=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TTC41P	NR_027249.1	n.331-862G>T		intron_variant	Intron 1 of 15

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293399	ENST00000388789.5	n.273-862G>T		intron_variant	Intron 1 of 1	1
ENSG00000293399	ENST00000548520.2	n.231-862G>T		intron_variant	Intron 1 of 9	5
ENSG00000293399	ENST00000548897.1	n.942-862G>T		intron_variant	Intron 4 of 4	5

Frequencies

GnomAD3 genomes AF: 0.0800 AC: 12163 AN: 152062 Hom.: 638 Cov.: 32

Gnomad AFR AF: 0.0997

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.0666

Gnomad ASJ AF: 0.0793

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.0284

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0656

Gnomad OTH AF: 0.0823

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0800 AC: 12179 AN: 152180 Hom.: 642 Cov.: 32 AF XY: 0.0807 AC XY: 6004 AN XY: 74412

African (AFR) AF: 0.0997 AC: 4135 AN: 41486

American (AMR) AF: 0.0664 AC: 1016 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0793 AC: 275 AN: 3466

East Asian (EAS) AF: 0.182 AC: 943 AN: 5174

South Asian (SAS) AF: 0.162 AC: 782 AN: 4826

European-Finnish (FIN) AF: 0.0284 AC: 301 AN: 10606

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0656 AC: 4465 AN: 68014

Other (OTH) AF: 0.0843 AC: 178 AN: 2112

Alfa AF: 0.0725 Hom.: 61

Bravo AF: 0.0830

Asia WGS AF: 0.150 AC: 522 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.5
DANN	Benign	0.79
PhyloP100		0.62

Splicing

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

Other links and lift over

dbSNP: rs11111839; hg19: chr12-104310723;