12-103924628-G-A

Variant names:

• chr12-103924628-G-A
• rs1165670
• ENST00000388789.5:n.272+5254C>T

Variant summary

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

The ENST00000388789.5(ENSG00000293399):​n.272+5254C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.707 in 152,062 control chromosomes in the GnomAD database, including 38,134 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 0.71 (38134 hom., cov: 31)
• Consequence: ENSG00000293399 ENST00000388789.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.776
• 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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.729 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000388789.5. 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
	TTC41P	NR_027249.1		n.330+5254C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000293399	ENST00000388789.5	TSL:1	n.272+5254C>T		intron	N/A
	ENSG00000293399	ENST00000548520.2	TSL:5	n.230+5254C>T		intron	N/A
	ENSG00000293399	ENST00000548897.1	TSL:5	n.788+865C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.707 AC: 107372 AN: 151944 Hom.: 38089 Cov.: 31

Gnomad AFR AF: 0.698

Gnomad AMI AF: 0.704

Gnomad AMR AF: 0.642

Gnomad ASJ AF: 0.656

Gnomad EAS AF: 0.642

Gnomad SAS AF: 0.644

Gnomad FIN AF: 0.731

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.735

Gnomad OTH AF: 0.714

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

GnomAD4 genome AF: 0.707 AC: 107476 AN: 152062 Hom.: 38134 Cov.: 31 AF XY: 0.704 AC XY: 52318 AN XY: 74348

African (AFR) AF: 0.699 AC: 28985 AN: 41470

American (AMR) AF: 0.642 AC: 9808 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.656 AC: 2277 AN: 3472

East Asian (EAS) AF: 0.644 AC: 3320 AN: 5156

South Asian (SAS) AF: 0.644 AC: 3107 AN: 4826

European-Finnish (FIN) AF: 0.731 AC: 7720 AN: 10560

Middle Eastern (MID) AF: 0.606 AC: 177 AN: 292

European-Non Finnish (NFE) AF: 0.735 AC: 49937 AN: 67976

Other (OTH) AF: 0.711 AC: 1503 AN: 2114

Alfa AF: 0.721 Hom.: 19676

Bravo AF: 0.701

Asia WGS AF: 0.626 AC: 2176 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.54
DANN	Benign	0.43
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs1165670; hg19: chr12-104318406;