NM_017735.5:c.397-970G>T

Variant names:

• chr2-32639300-G-T
• rs2710605
• NM_017735.5:c.397-970G>T

Variant summary

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

The NM_017735.5(TTC27):​c.397-970G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.767 in 152,172 control chromosomes in the GnomAD database, including 44,969 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 0.77 (44969 hom., cov: 33)
• Consequence: TTC27 NM_017735.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.335
• Publications: 6 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.805 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.397-970G>T		intron	N/A	NP_060205.3
	TTC27	NM_001193509.2		c.247-970G>T		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.397-970G>T		intron	N/A	ENSP00000313953.4
	TTC27	ENST00000448773.5	TSL:4	c.247-970G>T		intron	N/A	ENSP00000393327.1
	TTC27	ENST00000454690.1	TSL:3	n.88+10920G>T		intron	N/A	ENSP00000392883.1

Frequencies

GnomAD3 genomes AF: 0.768 AC: 116705 AN: 152054 Hom.: 44936 Cov.: 33

Gnomad AFR AF: 0.813

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.688

Gnomad ASJ AF: 0.782

Gnomad EAS AF: 0.629

Gnomad SAS AF: 0.783

Gnomad FIN AF: 0.797

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.763

Gnomad OTH AF: 0.756

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

GnomAD4 genome AF: 0.767 AC: 116782 AN: 152172 Hom.: 44969 Cov.: 33 AF XY: 0.766 AC XY: 56966 AN XY: 74390

African (AFR) AF: 0.813 AC: 33741 AN: 41518

American (AMR) AF: 0.687 AC: 10494 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.782 AC: 2714 AN: 3472

East Asian (EAS) AF: 0.630 AC: 3255 AN: 5166

South Asian (SAS) AF: 0.783 AC: 3784 AN: 4832

European-Finnish (FIN) AF: 0.797 AC: 8432 AN: 10584

Middle Eastern (MID) AF: 0.820 AC: 241 AN: 294

European-Non Finnish (NFE) AF: 0.763 AC: 51907 AN: 68008

Other (OTH) AF: 0.754 AC: 1593 AN: 2112

Alfa AF: 0.759 Hom.: 38016

Bravo AF: 0.760

Asia WGS AF: 0.735 AC: 2555 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.3
DANN	Benign	0.44
PhyloP100		0.34
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: rs2710605; hg19: chr2-32864367;