2-32812092-T-C

Position:

• chr2-32812092-T-C

Variant summary

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

The NM_017735.5(TTC27):​c.2197-412T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.413 in 152,040 control chromosomes in the GnomAD database, including 13,440 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 0.41 (13440 hom., cov: 32)
• Consequence: TTC27 NM_017735.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900

Genes affected

TTC27 (HGNC:25986): (tetratricopeptide repeat domain 27)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.568 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TTC27	NM_017735.5	c.2197-412T>C		intron_variant		ENST00000317907.9	NP_060205.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TTC27	ENST00000317907.9	c.2197-412T>C		intron_variant		1	NM_017735.5	ENSP00000313953	P1
TTC27	ENST00000428527.1	c.*435-412T>C		intron_variant, NMD_transcript_variant		3		ENSP00000398820
TTC27	ENST00000647819.1	c.*1402-412T>C		intron_variant, NMD_transcript_variant				ENSP00000497009

Frequencies

GnomAD3 genomes AF: 0.413 AC: 62786 AN: 151922 Hom.: 13418 Cov.: 32

Gnomad AFR AF: 0.489

Gnomad AMI AF: 0.461

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.523

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.587

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.413 AC: 62849 AN: 152040 Hom.: 13440 Cov.: 32 AF XY: 0.412 AC XY: 30615 AN XY: 74314

Gnomad4 AFR AF: 0.489

Gnomad4 AMR AF: 0.358

Gnomad4 ASJ AF: 0.523

Gnomad4 EAS AF: 0.361

Gnomad4 SAS AF: 0.586

Gnomad4 FIN AF: 0.287

Gnomad4 NFE AF: 0.384

Gnomad4 OTH AF: 0.421

Alfa AF: 0.399 Hom.: 12006

Bravo AF: 0.417

Asia WGS AF: 0.519 AC: 1803 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	3.9
DANN	Benign	0.88

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs927087; hg19: chr2-33037159;