chr7-75109047-C-T

Variant names:

• chr7-75109047-C-T
• rs782613958
• NM_001003795.3:c.83C>T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001003795.3(GTF2IRD2B):​c.83C>T​(p.Ser28Phe) variant causes a missense change. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S28C) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 12)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: GTF2IRD2B NM_001003795.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.08
• Publications: 0 publications found

Genes affected

GTF2IRD2B (HGNC:33125): (GTF2I repeat domain containing 2B) This gene encodes a glycosylated phosphoprotein with a leucine zipper motif, two helix-loop-helix motifs (I repeats) that are similar to domains found in the TFII-I family of transcription factors, one CHARLIE8 transposable element-like sequence, and a BED zinc finger. This gene lies within a region that is deleted in Williams-Beuren syndrome. Alternatively spliced variants which encode different protein isoforms have been described; however, not all variants have been fully characterized. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001003795.3. 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
	GTF2IRD2B	NM_001003795.3	MANE Select	c.83C>T	p.Ser28Phe	missense	Exon 2 of 16	NP_001003795.1	Q6EKJ0-1
	GTF2IRD2B	NM_001368302.1		c.569C>T	p.Ser190Phe	missense	Exon 2 of 16	NP_001355231.1
	GTF2IRD2B	NM_001368301.1		c.83C>T	p.Ser28Phe	missense	Exon 2 of 3	NP_001355230.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GTF2IRD2B	ENST00000472837.7	TSL:1 MANE Select	c.83C>T	p.Ser28Phe	missense	Exon 2 of 16	ENSP00000480524.1	Q6EKJ0-1
	GTF2IRD2B	ENST00000619142.4	TSL:1	c.83C>T	p.Ser28Phe	missense	Exon 2 of 16	ENSP00000480037.1	A0A087WW90
	GTF2IRD2B	ENST00000614064.4	TSL:1	c.83C>T	p.Ser28Phe	missense	Exon 2 of 3	ENSP00000481706.1

Frequencies

GnomAD3 genomes Cov.: 12

GnomAD2 exomes AF: 0.00000608 AC: 1 AN: 164410 AF XY: 0.0000115

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.0000566

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 676934 Hom.: 0 Cov.: 7 AF XY: 0.00 AC XY: 0 AN XY: 342308

African (AFR) AF: 0.00 AC: 0 AN: 31078

American (AMR) AF: 0.00 AC: 0 AN: 18386

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 12882

East Asian (EAS) AF: 0.00 AC: 0 AN: 6132

South Asian (SAS) AF: 0.00 AC: 0 AN: 48862

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 23608

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3558

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 502784

Other (OTH) AF: 0.00 AC: 0 AN: 29644

GnomAD4 genome Cov.: 12

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.77
BayesDel_addAF	Pathogenic	0.22	D
BayesDel_noAF	Uncertain	0.080
CADD	Pathogenic	30
DANN	Uncertain	1.0
DEOGEN2	Benign	0.11	T
Eigen	Uncertain	0.43
Eigen_PC	Uncertain	0.28
FATHMM_MKL	Uncertain	0.85	D
LIST_S2	Uncertain	0.94	D
M_CAP	Benign	0.022	T
MetaRNN	Uncertain	0.74	D
MetaSVM	Uncertain	-0.28	T
MutationAssessor	Uncertain	2.5	M
PhyloP100		4.1
PrimateAI	Uncertain	0.74	T
Sift4G	Pathogenic	0.0010	D
Polyphen		1.0	D
Vest4		0.82
MutPred		0.46		Loss of disorder (P = 0.0252)
MVP		0.099
ClinPred		0.88	D
GERP RS		3.0
Varity_R		0.25
gMVP		0.38
Mutation Taster		=89/11	polymorphism

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

Other links and lift over

dbSNP: rs782613958; hg19: chr7-74524839;