2-32723127-A-G

Variant names:

• chr2-32723127-A-G
• rs13029809
• NM_017735.5:c.1234-10701A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_017735.5(TTC27):​c.1234-10701A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 152,222 control chromosomes in the GnomAD database, including 1,663 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 0.13 (1663 hom., cov: 32)
• Consequence: TTC27 NM_017735.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.285
• Publications: 5 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.23 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.1234-10701A>G		intron	N/A	NP_060205.3
	TTC27	NM_001193509.2		c.1084-10701A>G		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.1234-10701A>G		intron	N/A	ENSP00000313953.4
	TTC27	ENST00000934659.1		c.1234-10701A>G		intron	N/A	ENSP00000604718.1
	TTC27	ENST00000956005.1		c.1213-10701A>G		intron	N/A	ENSP00000626064.1

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19881 AN: 152104 Hom.: 1660 Cov.: 32

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.0871

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.000960

Gnomad SAS AF: 0.0782

Gnomad FIN AF: 0.0829

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.0982

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.131 AC: 19909 AN: 152222 Hom.: 1663 Cov.: 32 AF XY: 0.128 AC XY: 9511 AN XY: 74446

African (AFR) AF: 0.234 AC: 9700 AN: 41514

American (AMR) AF: 0.0871 AC: 1332 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.157 AC: 545 AN: 3470

East Asian (EAS) AF: 0.000963 AC: 5 AN: 5194

South Asian (SAS) AF: 0.0777 AC: 374 AN: 4814

European-Finnish (FIN) AF: 0.0829 AC: 879 AN: 10606

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.0982 AC: 6680 AN: 68008

Other (OTH) AF: 0.123 AC: 260 AN: 2112

Alfa AF: 0.104 Hom.: 456

Bravo AF: 0.135

Asia WGS AF: 0.0490 AC: 169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.7
DANN	Benign	0.56
PhyloP100		0.28
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: rs13029809; hg19: chr2-32948194;