rs1339110

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_203395.3(IYD):​c.178+8209C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 152,122 control chromosomes in the GnomAD database, including 3,552 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 0.15 ( 3552 hom., cov: 32)

Consequence

IYD
NM_203395.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.293
Variant links:
Genes affected
IYD (HGNC:21071): (iodotyrosine deiodinase) This gene encodes an enzyme that catalyzes the oxidative NADPH-dependent deiodination of mono- and diiodotyrosine, which are the halogenated byproducts of thyroid hormone production. The N-terminus of the protein functions as a membrane anchor. Mutations in this gene cause congenital hypothyroidism due to dyshormonogenesis type 4, which is also referred to as deiodinase deficiency, or iodotyrosine dehalogenase deficiency, or thyroid hormonogenesis type 4. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2009]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.373 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
IYDNM_203395.3 linkuse as main transcriptc.178+8209C>G intron_variant ENST00000344419.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
IYDENST00000344419.8 linkuse as main transcriptc.178+8209C>G intron_variant 1 NM_203395.3 P1Q6PHW0-1

Frequencies

GnomAD3 genomes
AF:
0.152
AC:
23154
AN:
152004
Hom.:
3530
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.378
Gnomad AMI
AF:
0.177
Gnomad AMR
AF:
0.134
Gnomad ASJ
AF:
0.0642
Gnomad EAS
AF:
0.298
Gnomad SAS
AF:
0.139
Gnomad FIN
AF:
0.0179
Gnomad MID
AF:
0.0633
Gnomad NFE
AF:
0.0351
Gnomad OTH
AF:
0.139
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.153
AC:
23219
AN:
152122
Hom.:
3552
Cov.:
32
AF XY:
0.152
AC XY:
11305
AN XY:
74358
show subpopulations
Gnomad4 AFR
AF:
0.378
Gnomad4 AMR
AF:
0.134
Gnomad4 ASJ
AF:
0.0642
Gnomad4 EAS
AF:
0.299
Gnomad4 SAS
AF:
0.138
Gnomad4 FIN
AF:
0.0179
Gnomad4 NFE
AF:
0.0351
Gnomad4 OTH
AF:
0.144
Alfa
AF:
0.0940
Hom.:
228
Bravo
AF:
0.174
Asia WGS
AF:
0.232
AC:
809
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
3.9
DANN
Benign
0.52

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1339110; hg19: chr6-150698554; API