2-74493928-A-G

Position:

• chr2-74493928-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_022492.6(TTC31):​c.*710A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 152,204 control chromosomes in the GnomAD database, including 16,030 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 0.36 (16029 hom., cov: 33)
  • Exomes 𝑓: 0.19 (1 hom.)
• Consequence: TTC31 NM_022492.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00100

Genes affected

TTC31 (HGNC:25759): (tetratricopeptide repeat domain 31)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.804 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TTC31	NM_022492.6	c.*710A>G		3_prime_UTR_variant	13/13	ENST00000233623.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TTC31	ENST00000233623.11	c.*710A>G		3_prime_UTR_variant	13/13	1	NM_022492.6	P1

Frequencies

GnomAD3 genomes AF: 0.358 AC: 54385 AN: 152054 Hom.: 15990 Cov.: 33

Gnomad AFR AF: 0.771

Gnomad AMI AF: 0.233

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.825

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.305

GnomAD4 exome AF: 0.188 AC: 6 AN: 32 Hom.: 1 Cov.: 0 AF XY: 0.192 AC XY: 5 AN XY: 26

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.208

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.358 AC: 54483 AN: 152172 Hom.: 16029 Cov.: 33 AF XY: 0.357 AC XY: 26585 AN XY: 74398

Gnomad4 AFR AF: 0.772

Gnomad4 AMR AF: 0.277

Gnomad4 ASJ AF: 0.150

Gnomad4 EAS AF: 0.825

Gnomad4 SAS AF: 0.311

Gnomad4 FIN AF: 0.140

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.306

Alfa AF: 0.188 Hom.: 4163

Bravo AF: 0.392

Asia WGS AF: 0.579 AC: 2012 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.9
DANN	Benign	0.67

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: rs2301984; hg19: chr2-74721055;