16-11745470-G-T

Variant names:

• chr16-11745470-G-T
• rs4780401
• ENST00000789294.1:n.110+2244G>T

Variant summary

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

The ENST00000789294.1(TXNDC11-AS1):​n.110+2244G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.562 in 151,748 control chromosomes in the GnomAD database, including 24,310 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 0.56 (24310 hom., cov: 32)
• Consequence: TXNDC11-AS1 ENST00000789294.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.629
• Publications: 29 publications found

Genes affected

TXNDC11-AS1 (HGNC:56375): (TXNDC11 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TXNDC11-AS1	ENST00000789294.1	n.110+2244G>T		intron_variant	Intron 1 of 2
TXNDC11-AS1	ENST00000789295.1	n.176+2244G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.562 AC: 85185 AN: 151630 Hom.: 24286 Cov.: 32

Gnomad AFR AF: 0.555

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.714

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.568

Gnomad FIN AF: 0.620

Gnomad MID AF: 0.685

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.559

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

GnomAD4 genome AF: 0.562 AC: 85254 AN: 151748 Hom.: 24310 Cov.: 32 AF XY: 0.562 AC XY: 41658 AN XY: 74156

African (AFR) AF: 0.555 AC: 22930 AN: 41346

American (AMR) AF: 0.422 AC: 6431 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.714 AC: 2475 AN: 3468

East Asian (EAS) AF: 0.409 AC: 2099 AN: 5128

South Asian (SAS) AF: 0.569 AC: 2736 AN: 4812

European-Finnish (FIN) AF: 0.620 AC: 6520 AN: 10522

Middle Eastern (MID) AF: 0.685 AC: 200 AN: 292

European-Non Finnish (NFE) AF: 0.590 AC: 40103 AN: 67916

Other (OTH) AF: 0.564 AC: 1189 AN: 2108

Alfa AF: 0.573 Hom.: 42337

Bravo AF: 0.542

Asia WGS AF: 0.504 AC: 1754 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.58
DANN	Benign	0.20
PhyloP100		-0.63

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4780401; hg19: chr16-11839326;