2-32812092-T-C

Variant names:

• chr2-32812092-T-C
• rs927087
• NM_017735.5:c.2197-412T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017735.5. 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
	TTC27	NM_017735.5	MANE Select	c.2197-412T>C		intron	N/A	NP_060205.3
	TTC27	NM_001193509.2		c.2047-412T>C		intron	N/A	NP_001180438.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TTC27	ENST00000317907.9	TSL:1 MANE Select	c.2197-412T>C		intron	N/A	ENSP00000313953.4
	TTC27	ENST00000934659.1		c.2218-412T>C		intron	N/A	ENSP00000604718.1
	TTC27	ENST00000956005.1		c.2176-412T>C		intron	N/A	ENSP00000626064.1

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

African (AFR) AF: 0.489 AC: 20261 AN: 41454

American (AMR) AF: 0.358 AC: 5463 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.523 AC: 1815 AN: 3470

East Asian (EAS) AF: 0.361 AC: 1864 AN: 5162

South Asian (SAS) AF: 0.586 AC: 2826 AN: 4822

European-Finnish (FIN) AF: 0.287 AC: 3037 AN: 10582

Middle Eastern (MID) AF: 0.548 AC: 160 AN: 292

European-Non Finnish (NFE) AF: 0.384 AC: 26115 AN: 67958

Other (OTH) AF: 0.421 AC: 889 AN: 2112

Alfa AF: 0.399 Hom.: 14341

Bravo AF: 0.417

Asia WGS AF: 0.519 AC: 1803 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	3.9
DANN	Benign	0.88
PhyloP100		0.0090
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs927087; hg19: chr2-33037159;