rs1565970

Variant names:

• chr14-52431358-A-C
• rs1565970
• NM_020784.3:c.*946T>G

Your query was ambiguous. Multiple possible variants found:

• chr14-52431358-A-C
• chr14-52431358-A-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_020784.3(TXNDC16):​c.*946T>G variant causes a 3 prime UTR 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: 33)
• Consequence: TXNDC16 NM_020784.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.342
• Publications: 11 publications found

Genes affected

TXNDC16 (HGNC:19965): (thioredoxin domain containing 16) Located in endoplasmic reticulum lumen. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020784.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TXNDC16	NM_020784.3	MANE Select	c.*946T>G		3_prime_UTR	Exon 21 of 21	NP_065835.2	Q9P2K2
	TXNDC16	NM_001160047.2		c.*946T>G		3_prime_UTR	Exon 21 of 21	NP_001153519.1	B7ZME4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TXNDC16	ENST00000281741.9	TSL:1 MANE Select	c.*946T>G		3_prime_UTR	Exon 21 of 21	ENSP00000281741.4	Q9P2K2
	TXNDC16	ENST00000936707.1		c.*946T>G		3_prime_UTR	Exon 21 of 21	ENSP00000606766.1
	TXNDC16	ENST00000956219.1		c.*946T>G		3_prime_UTR	Exon 22 of 22	ENSP00000626278.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 740

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.1
DANN	Benign	0.62
PhyloP100		0.34

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: rs1565970; hg19: chr14-52898076;