14-81168979-C-T

Variant names:

• chr14-81168979-C-T
• rs10131728
• ENST00000646052.2:n.321+1130G>A

Variant summary

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

The ENST00000646052.2(TSHR-AS1):​n.321+1130G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 152,200 control chromosomes in the GnomAD database, including 1,172 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 0.11 (1172 hom., cov: 33)
• Consequence: TSHR-AS1 ENST00000646052.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.681
• Publications: 5 publications found

Genes affected

TSHR-AS1 (HGNC:58172):

ENSG00000286686 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000646052.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TSHR-AS1	ENST00000646052.2		n.321+1130G>A		intron	N/A
	TSHR-AS1	ENST00000646928.1		n.306+1130G>A		intron	N/A
	TSHR-AS1	ENST00000652775.1		n.321+1130G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17194 AN: 152082 Hom.: 1172 Cov.: 33

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.0842

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.00674

Gnomad SAS AF: 0.0439

Gnomad FIN AF: 0.0763

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0951

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.113 AC: 17205 AN: 152200 Hom.: 1172 Cov.: 33 AF XY: 0.107 AC XY: 7985 AN XY: 74414

African (AFR) AF: 0.177 AC: 7340 AN: 41504

American (AMR) AF: 0.0840 AC: 1285 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 612 AN: 3472

East Asian (EAS) AF: 0.00695 AC: 36 AN: 5180

South Asian (SAS) AF: 0.0433 AC: 209 AN: 4824

European-Finnish (FIN) AF: 0.0763 AC: 808 AN: 10594

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.0951 AC: 6468 AN: 68008

Other (OTH) AF: 0.117 AC: 247 AN: 2110

Alfa AF: 0.106 Hom.: 1251

Bravo AF: 0.118

Asia WGS AF: 0.0400 AC: 139 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.42
PhyloP100		0.68

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: rs10131728;

hg19: chr14-81635323;