rs4858119

Variant names:

• chr3-24497615-T-G
• rs4858119
• ENST00000432368.2:n.406-1917T>G

Variant summary

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

The ENST00000432368.2(THRB-AS1):​n.406-1917T>G variant causes a intron 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 ENST00000432368.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.161
• Publications: 2 publications found

Genes affected

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

ENSG00000272554 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000432368.2. 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
	THRB-AS1	NR_046244.1		n.406-1917T>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	THRB-AS1	ENST00000432368.2	TSL:2	n.406-1917T>G		intron	N/A
	ENSG00000272554	ENST00000608068.2	TSL:5	n.301-602A>C		intron	N/A
	THRB-AS1	ENST00000608893.6	TSL:5	n.717+797T>G		intron	N/A

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

African (AFR) AF: 0.788 AC: 32680 AN: 41490

American (AMR) AF: 0.540 AC: 8241 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.563 AC: 1955 AN: 3472

East Asian (EAS) AF: 0.444 AC: 2285 AN: 5142

South Asian (SAS) AF: 0.508 AC: 2438 AN: 4800

European-Finnish (FIN) AF: 0.526 AC: 5545 AN: 10534

Middle Eastern (MID) AF: 0.582 AC: 170 AN: 292

European-Non Finnish (NFE) AF: 0.582 AC: 39585 AN: 67964

Other (OTH) AF: 0.633 AC: 1335 AN: 2110

Alfa AF: 0.609 Hom.: 3752

Bravo AF: 0.632

Asia WGS AF: 0.505 AC: 1757 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.46
PhyloP100		-0.16

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4858119;

hg19: chr3-24539106;