3-24608803-A-C

Variant names:

• chr3-24608803-A-C
• rs2076993
• ENST00000630391.1:n.596+19730A>C

Variant summary

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

The ENST00000630391.1(THRB-AS1):​n.596+19730A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 151,774 control chromosomes in the GnomAD database, including 9,127 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 0.33 (9127 hom., cov: 31)
• Consequence: THRB-AS1 ENST00000630391.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.364
• Publications: 3 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.462 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000630391.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	THRB-AS1	ENST00000630391.1	TSL:5	n.596+19730A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50775 AN: 151656 Hom.: 9128 Cov.: 31

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.424

Gnomad EAS AF: 0.478

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.347

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

GnomAD4 genome AF: 0.335 AC: 50780 AN: 151774 Hom.: 9127 Cov.: 31 AF XY: 0.336 AC XY: 24882 AN XY: 74120

African (AFR) AF: 0.208 AC: 8606 AN: 41444

American (AMR) AF: 0.307 AC: 4677 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.424 AC: 1470 AN: 3470

East Asian (EAS) AF: 0.478 AC: 2441 AN: 5112

South Asian (SAS) AF: 0.434 AC: 2083 AN: 4802

European-Finnish (FIN) AF: 0.396 AC: 4156 AN: 10496

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.388 AC: 26350 AN: 67900

Other (OTH) AF: 0.347 AC: 732 AN: 2108

Alfa AF: 0.346 Hom.: 3860

Bravo AF: 0.319

Asia WGS AF: 0.484 AC: 1680 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	14
DANN	Benign	0.85
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs2076993; hg19: chr3-24650294;