2-32685471-T-C

Position:

• chr2-32685471-T-C

Variant summary

Our verdict is Benign. Variant got -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

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=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.866 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TTC27	NM_017735.5	c.1119+6549T>C		intron_variant		ENST00000317907.9	NP_060205.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TTC27	ENST00000317907.9	c.1119+6549T>C		intron_variant		1	NM_017735.5	ENSP00000313953.4
TTC27	ENST00000438654.1	c.45+6549T>C		intron_variant		3		ENSP00000409230.1
TTC27	ENST00000454690.1	n.*29+6549T>C		intron_variant		3		ENSP00000392883.1
TTC27	ENST00000647819.1	n.*324+6549T>C		intron_variant				ENSP00000497009.1

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

Gnomad4 AFR AF: 0.820

Gnomad4 AMR AF: 0.788

Gnomad4 ASJ AF: 0.916

Gnomad4 EAS AF: 0.787

Gnomad4 SAS AF: 0.889

Gnomad4 FIN AF: 0.856

Gnomad4 NFE AF: 0.845

Gnomad4 OTH AF: 0.837

Alfa AF: 0.831 Hom.: 18474

Bravo AF: 0.827

Asia WGS AF: 0.845 AC: 2937 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.1
DANN	Benign	0.84

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: rs1979148; hg19: chr2-32910538;