chr3-24667383-A-G

Variant names:

• chr3-24667383-A-G
• rs6767967
• ENST00000630391.1:n.597-12933A>G

Variant summary

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

The ENST00000630391.1(THRB-AS1):​n.597-12933A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.576 in 152,004 control chromosomes in the GnomAD database, including 25,951 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 0.58 (25951 hom., cov: 32)
• Consequence: THRB-AS1 ENST00000630391.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• 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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.721 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.597-12933A>G		intron_variant	Intron 4 of 4	5

Frequencies

GnomAD3 genomes AF: 0.576 AC: 87520 AN: 151886 Hom.: 25924 Cov.: 32

Gnomad AFR AF: 0.688

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.740

Gnomad SAS AF: 0.654

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.554

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

GnomAD4 genome AF: 0.576 AC: 87594 AN: 152004 Hom.: 25951 Cov.: 32 AF XY: 0.580 AC XY: 43104 AN XY: 74286

African (AFR) AF: 0.689 AC: 28546 AN: 41448

American (AMR) AF: 0.508 AC: 7756 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.537 AC: 1862 AN: 3470

East Asian (EAS) AF: 0.740 AC: 3836 AN: 5182

South Asian (SAS) AF: 0.653 AC: 3145 AN: 4818

European-Finnish (FIN) AF: 0.577 AC: 6090 AN: 10556

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.512 AC: 34804 AN: 67954

Other (OTH) AF: 0.553 AC: 1167 AN: 2110

Alfa AF: 0.528 Hom.: 30697

Bravo AF: 0.570

Asia WGS AF: 0.712 AC: 2476 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.17
DANN	Benign	0.48
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs6767967; hg19: chr3-24708874;