rs1165670

Positions:

• chr12-103924628-G-A

Variant summary

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

The ENST00000388789.4(TTC41P):​n.250+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: TTC41P ENST00000388789.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.776

Genes affected

TTC41P (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TTC41P	NR_027249.1	n.330+5254C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TTC41P	ENST00000388789.4	n.250+5254C>T		intron_variant		1
TTC41P	ENST00000548897.1	n.788+865C>T		intron_variant		5

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

Gnomad4 AFR AF: 0.699

Gnomad4 AMR AF: 0.642

Gnomad4 ASJ AF: 0.656

Gnomad4 EAS AF: 0.644

Gnomad4 SAS AF: 0.644

Gnomad4 FIN AF: 0.731

Gnomad4 NFE AF: 0.735

Gnomad4 OTH AF: 0.711

Alfa AF: 0.721 Hom.: 17692

Bravo AF: 0.701

Asia WGS AF: 0.626 AC: 2176 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1165670; hg19: chr12-104318406;