rs11111839

Positions:

• chr12-103916945-C-A

Variant summary

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

The NR_027249.1(TTC41P):​n.331-862G>T variant causes a intron, non coding transcript 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: TTC41P NR_027249.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.623

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
TTC41P	NR_027249.1	n.331-862G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000388789.4	n.251-862G>T		intron_variant, non_coding_transcript_variant		1
	ENST00000548520.2	n.231-862G>T		intron_variant, non_coding_transcript_variant		5
	ENST00000548897.1	n.942-862G>T		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.0997

Gnomad4 AMR AF: 0.0664

Gnomad4 ASJ AF: 0.0793

Gnomad4 EAS AF: 0.182

Gnomad4 SAS AF: 0.162

Gnomad4 FIN AF: 0.0284

Gnomad4 NFE AF: 0.0656

Gnomad4 OTH AF: 0.0843

Alfa AF: 0.0708 Hom.: 56

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11111839; hg19: chr12-104310723;