rs2076993

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr3-24608803-A-C
• chr3-24608803-A-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.462 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
THRB-AS1	ENST00000630391.1	n.596+19730A>C		intron_variant	Intron 4 of 4	5

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

Gnomad4 AFR AF: 0.208

Gnomad4 AMR AF: 0.307

Gnomad4 ASJ AF: 0.424

Gnomad4 EAS AF: 0.478

Gnomad4 SAS AF: 0.434

Gnomad4 FIN AF: 0.396

Gnomad4 NFE AF: 0.388

Gnomad4 OTH AF: 0.347

Alfa AF: 0.347 Hom.: 3131

Bravo AF: 0.319

Asia WGS AF: 0.484 AC: 1680 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2076993; hg19: chr3-24650294;