chr12-103928406-G-A

Position:

• chr12-103928406-G-A

Variant summary

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

The NR_027249.1(TTC41P):​n.330+1476C>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 0.67 in 152,072 control chromosomes in the GnomAD database, including 34,721 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 0.67 (34711 hom., cov: 32)
  • Exomes 𝑓: 0.67 (10 hom.)
• Consequence: TTC41P NR_027249.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.07

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.827 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TTC41P	NR_027249.1	n.330+1476C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000388789.4	n.250+1476C>T		intron_variant, non_coding_transcript_variant		1
	ENST00000548520.2	n.230+1476C>T		intron_variant, non_coding_transcript_variant		5
	ENST00000548897.1	n.471C>T		non_coding_transcript_exon_variant	2/5	5

Frequencies

GnomAD3 genomes AF: 0.670 AC: 101730 AN: 151908 Hom.: 34672 Cov.: 32

Gnomad AFR AF: 0.750

Gnomad AMI AF: 0.728

Gnomad AMR AF: 0.712

Gnomad ASJ AF: 0.695

Gnomad EAS AF: 0.848

Gnomad SAS AF: 0.834

Gnomad FIN AF: 0.600

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.596

Gnomad OTH AF: 0.641

GnomAD4 exome AF: 0.674 AC: 31 AN: 46 Hom.: 10 Cov.: 0 AF XY: 0.694 AC XY: 25 AN XY: 36

Gnomad4 AFR exome AF: 1.00

Gnomad4 SAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.656

Gnomad4 OTH exome AF: 0.667

GnomAD4 genome AF: 0.670 AC: 101830 AN: 152026 Hom.: 34711 Cov.: 32 AF XY: 0.676 AC XY: 50244 AN XY: 74272

Gnomad4 AFR AF: 0.750

Gnomad4 AMR AF: 0.713

Gnomad4 ASJ AF: 0.695

Gnomad4 EAS AF: 0.848

Gnomad4 SAS AF: 0.835

Gnomad4 FIN AF: 0.600

Gnomad4 NFE AF: 0.596

Gnomad4 OTH AF: 0.646

Alfa AF: 0.646 Hom.: 4481

Bravo AF: 0.680

Asia WGS AF: 0.835 AC: 2902 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	11
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1165678; hg19: chr12-104322184;