chr1-52051740-A-C

Position:

• chr1-52051740-A-C

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000371626.9(TXNDC12):​c.97+3260T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
• Consequence: TXNDC12 ENST00000371626.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.609

Genes affected

TXNDC12 (HGNC:24626): (thioredoxin domain containing 12) This gene encodes a member of the thioredoxin superfamily. Members of this family are characterized by a conserved active motif called the thioredoxin fold that catalyzes disulfide bond formation and isomerization. This protein localizes to the endoplasmic reticulum and has a single atypical active motif. The encoded protein is mainly involved in catalyzing native disulfide bond formation and displays activity similar to protein-disulfide isomerases. This protein may play a role in defense against endoplasmic reticulum stress. Alternate splicing results in both coding and non-coding variants. [provided by RefSeq, Mar 2012]

TXNDC12-AS1 (HGNC:30008): (TXNDC12 antisense RNA 1)

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TXNDC12	NM_015913.4	c.97+3260T>G		intron_variant		ENST00000371626.9	NP_056997.1
TXNDC12-AS1	NR_126385.1	n.49-44A>C		intron_variant, non_coding_transcript_variant
TXNDC12	NR_046405.1	n.1172+3260T>G		intron_variant, non_coding_transcript_variant
TXNDC12	NR_046406.1	n.1172+3260T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TXNDC12	ENST00000371626.9	c.97+3260T>G		intron_variant		1	NM_015913.4	ENSP00000360688	P1
TXNDC12-AS1	ENST00000428794.1	n.49-44A>C		intron_variant, non_coding_transcript_variant		3
TXNDC12	ENST00000610127.2	c.97+3260T>G		intron_variant		2		ENSP00000476401
TXNDC12	ENST00000472624.5	c.97+3260T>G		intron_variant, NMD_transcript_variant		5		ENSP00000477120

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.4
DANN	Benign	0.63

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: rs7529324; hg19: chr1-52517412;