2-32639300-G-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.805 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TTC27	NM_017735.5	c.397-970G>T		intron_variant	Intron 3 of 19	ENST00000317907.9	NP_060205.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TTC27	ENST00000317907.9	c.397-970G>T		intron_variant	Intron 3 of 19	1	NM_017735.5	ENSP00000313953.4
TTC27	ENST00000448773.5	c.247-970G>T		intron_variant	Intron 3 of 3	4		ENSP00000393327.1
TTC27	ENST00000454690.1	n.88+10920G>T		intron_variant	Intron 1 of 3	3		ENSP00000392883.1
TTC27	ENST00000647819.1	n.397-970G>T		intron_variant	Intron 3 of 21			ENSP00000497009.1

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

Gnomad4 AFR AF: 0.813

Gnomad4 AMR AF: 0.687

Gnomad4 ASJ AF: 0.782

Gnomad4 EAS AF: 0.630

Gnomad4 SAS AF: 0.783

Gnomad4 FIN AF: 0.797

Gnomad4 NFE AF: 0.763

Gnomad4 OTH AF: 0.754

Alfa AF: 0.757 Hom.: 32081

Bravo AF: 0.760

Asia WGS AF: 0.735 AC: 2555 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.3
DANN	Benign	0.44

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: rs2710605; hg19: chr2-32864367;