2-32685471-T-C

Variant names:

• chr2-32685471-T-C
• rs1979148
• NM_017735.5:c.1119+6549T>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.1119+6549T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.834 in 152,096 control chromosomes in the GnomAD database, including 52,968 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 0.83 (52968 hom., cov: 32)
• Consequence: TTC27 NM_017735.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.739
• Publications: 4 publications found

Genes affected

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

ENSG00000295137 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.866 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.1119+6549T>C		intron	N/A	NP_060205.3
	TTC27	NM_001193509.2		c.969+6549T>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.1119+6549T>C		intron	N/A	ENSP00000313953.4
	TTC27	ENST00000438654.1	TSL:3	c.45+6549T>C		intron	N/A	ENSP00000409230.1
	TTC27	ENST00000454690.1	TSL:3	n.*29+6549T>C		intron	N/A	ENSP00000392883.1

Frequencies

GnomAD3 genomes AF: 0.834 AC: 126813 AN: 151978 Hom.: 52937 Cov.: 32

Gnomad AFR AF: 0.820

Gnomad AMI AF: 0.864

Gnomad AMR AF: 0.789

Gnomad ASJ AF: 0.916

Gnomad EAS AF: 0.786

Gnomad SAS AF: 0.889

Gnomad FIN AF: 0.856

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.845

Gnomad OTH AF: 0.835

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

GnomAD4 genome AF: 0.834 AC: 126892 AN: 152096 Hom.: 52968 Cov.: 32 AF XY: 0.834 AC XY: 62011 AN XY: 74378

African (AFR) AF: 0.820 AC: 33996 AN: 41464

American (AMR) AF: 0.788 AC: 12037 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.916 AC: 3177 AN: 3470

East Asian (EAS) AF: 0.787 AC: 4080 AN: 5184

South Asian (SAS) AF: 0.889 AC: 4281 AN: 4818

European-Finnish (FIN) AF: 0.856 AC: 9050 AN: 10576

Middle Eastern (MID) AF: 0.925 AC: 272 AN: 294

European-Non Finnish (NFE) AF: 0.845 AC: 57445 AN: 67986

Other (OTH) AF: 0.837 AC: 1771 AN: 2116

Alfa AF: 0.834 Hom.: 22906

Bravo AF: 0.827

Asia WGS AF: 0.845 AC: 2937 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.1
DANN	Benign	0.84
PhyloP100		-0.74
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: rs1979148; hg19: chr2-32910538;