rs2301984

Variant names:

• chr2-74493928-A-G
• rs2301984
• ENST00000424122.5:n.*1810A>G

Variant summary

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

The ENST00000424122.5(TTC31):​n.*1810A>G variant causes a non coding transcript exon 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 ENST00000424122.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00100
• Publications: 15 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
TTC31	NM_022492.6	c.*710A>G		3_prime_UTR_variant	Exon 13 of 13	ENST00000233623.11	NP_071937.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TTC31	ENST00000233623.11	c.*710A>G		3_prime_UTR_variant	Exon 13 of 13	1	NM_022492.6	ENSP00000233623.6

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.208 AC: 5 AN: 24

Other (OTH) AF: 0.250 AC: 1 AN: 4

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

African (AFR) AF: 0.772 AC: 32010 AN: 41490

American (AMR) AF: 0.277 AC: 4233 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 521 AN: 3472

East Asian (EAS) AF: 0.825 AC: 4275 AN: 5182

South Asian (SAS) AF: 0.311 AC: 1502 AN: 4826

European-Finnish (FIN) AF: 0.140 AC: 1484 AN: 10592

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.140 AC: 9537 AN: 67998

Other (OTH) AF: 0.306 AC: 647 AN: 2114

Alfa AF: 0.211 Hom.: 7151

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
PhyloP100		0.0010
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: rs2301984; hg19: chr2-74721055;