Variant 17-7618382-T-C details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001289114.2(SHBG):c.-62+4271T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.478 in 151,456 control chromosomes in the GnomAD database, including 18,302 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 0.48 ( 18302 hom., cov: 29)

Consequence

SHBG
NM_001289114.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.46

Variant links:

Genes affected

SHBG (HGNC:10839): (sex hormone binding globulin) This gene encodes a steroid binding protein that was first described as a plasma protein secreted by the liver but is now thought to participate in the regulation of steroid responses. The encoded protein transports androgens and estrogens in the blood, binding each steroid molecule as a dimer formed from identical or nearly identical monomers. Polymorphisms in this gene have been associated with polycystic ovary syndrome and type 2 diabetes mellitus. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]

SHBG links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.03).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.618 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SHBG	NM_001289114.2 link	c.-62+4271T>C		intron_variant			NP_001276043.1	P04278I3L145

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	Protein	UniProt
SHBG	ENST00000575314.5 link	c.-62+4271T>C	intron_variant	1	ENSP00000458559.1	I3L145
SHBG	ENST00000572262.5 link	c.-62+4271T>C	intron_variant	1	ENSP00000459999.1	I3L2X4
SHBG	ENST00000574539.5 link	c.-62+4271T>C	intron_variant	1	ENSP00000458181.1	P04278-2

Frequencies

GnomAD3 genomes

AF:

0.478

AC:

72286

AN:

151338

Hom.:

18292

Cov.:

show subpopulations

Gnomad AFR

AF:

0.307

Gnomad AMI

AF:

0.538

Gnomad AMR

AF:

0.432

Gnomad ASJ

AF:

0.648

Gnomad EAS

AF:

0.430

Gnomad SAS

AF:

0.637

Gnomad FIN

AF:

0.487

Gnomad MID

AF:

0.633

Gnomad NFE

AF:

0.571

Gnomad OTH

AF:

0.500

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

GnomAD4 genome

AF:

0.478

AC:

72340

AN:

151456

Hom.:

18302

Cov.:

AF XY:

0.477

AC XY:

35267

AN XY:

73972

show subpopulations

Gnomad4 AFR

AF:

0.308

Gnomad4 AMR

AF:

0.432

Gnomad4 ASJ

AF:

0.648

Gnomad4 EAS

AF:

0.430

Gnomad4 SAS

AF:

0.637

Gnomad4 FIN

AF:

0.487

Gnomad4 NFE

AF:

0.571

Gnomad4 OTH

AF:

0.500

Alfa

AF:

0.500

Hom.:

2358

Bravo

AF:

0.464

Asia WGS

AF:

0.513

AC:

1782

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

0.86

DANN

Benign

0.23

Splicing

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over