rs4858119

Positions:

• chr3-24497615-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_046244.1(THRB-AS1):​n.406-1917T>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.624 in 151,970 control chromosomes in the GnomAD database, including 30,501 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 0.62 (30501 hom., cov: 31)
• Consequence: THRB-AS1 NR_046244.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.161

Genes affected

(HGNC:):

THRB-AS1 (HGNC:44515): (THRB antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.781 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
THRB-AS1	NR_046244.1	n.406-1917T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000685164.2	n.208-602A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.624 AC: 94767 AN: 151852 Hom.: 30484 Cov.: 31

Gnomad AFR AF: 0.788

Gnomad AMI AF: 0.655

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.445

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.526

Gnomad MID AF: 0.583

Gnomad NFE AF: 0.583

Gnomad OTH AF: 0.637

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

GnomAD4 genome AF: 0.624 AC: 94827 AN: 151970 Hom.: 30501 Cov.: 31 AF XY: 0.616 AC XY: 45767 AN XY: 74252

Gnomad4 AFR AF: 0.788

Gnomad4 AMR AF: 0.540

Gnomad4 ASJ AF: 0.563

Gnomad4 EAS AF: 0.444

Gnomad4 SAS AF: 0.508

Gnomad4 FIN AF: 0.526

Gnomad4 NFE AF: 0.582

Gnomad4 OTH AF: 0.633

Alfa AF: 0.602 Hom.: 3510

Bravo AF: 0.632

Asia WGS AF: 0.505 AC: 1757 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4858119; hg19: chr3-24539106;