2-99306504-C-T

Variant names:

• chr2-99306504-C-T
• rs6722617
• ENST00000424491.5:n.*293-14622C>T

Variant summary

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

The ENST00000424491.5(ENSG00000241962):​n.*293-14622C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.602 in 151,494 control chromosomes in the GnomAD database, including 28,214 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 0.60 (28214 hom., cov: 32)
• Consequence: ENSG00000241962 ENST00000424491.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.652
• Publications: 4 publications found

Genes affected

ENSG00000241962 (HGNC:):

TXNDC9 (HGNC:24110): (thioredoxin domain containing 9) The protein encoded by this gene is a member of the thioredoxin family. The exact function of this protein is not known but it is associated with cell differentiation. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.677 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TXNDC9	XM_017003147.3	c.*269G>A		3_prime_UTR_variant	Exon 5 of 5		XP_016858636.1
LOC107985923	XR_007087152.1	n.126-14622C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000241962	ENST00000424491.5	n.*293-14622C>T		intron_variant	Intron 11 of 13	2		ENSP00000390891.1

Frequencies

GnomAD3 genomes AF: 0.602 AC: 91160 AN: 151374 Hom.: 28206 Cov.: 32

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.648

Gnomad ASJ AF: 0.819

Gnomad EAS AF: 0.696

Gnomad SAS AF: 0.644

Gnomad FIN AF: 0.558

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.658

Gnomad OTH AF: 0.656

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.602 AC: 91196 AN: 151494 Hom.: 28214 Cov.: 32 AF XY: 0.601 AC XY: 44480 AN XY: 74000

African (AFR) AF: 0.465 AC: 19249 AN: 41386

American (AMR) AF: 0.648 AC: 9897 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.819 AC: 2828 AN: 3452

East Asian (EAS) AF: 0.696 AC: 3573 AN: 5132

South Asian (SAS) AF: 0.645 AC: 3104 AN: 4814

European-Finnish (FIN) AF: 0.558 AC: 5769 AN: 10332

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.658 AC: 44632 AN: 67802

Other (OTH) AF: 0.657 AC: 1388 AN: 2114

Alfa AF: 0.644 Hom.: 26526

Bravo AF: 0.604

Asia WGS AF: 0.646 AC: 2250 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.8
DANN	Benign	0.23
PhyloP100		-0.65

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: rs6722617; hg19: chr2-99922967; COSMIC: COSV68215278;