rs10516527

Variant names:

• chr4-105813189-A-G
• rs10516527
• NM_001370181.1:c.1241-9765A>G

Variant summary

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

The NM_001370181.1(GSTCD):​c.1241-9765A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0538 in 152,104 control chromosomes in the GnomAD database, including 251 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 0.054 (251 hom., cov: 32)
• Consequence: GSTCD NM_001370181.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.592
• Publications: 5 publications found

Genes affected

GSTCD (HGNC:25806): (glutathione S-transferase C-terminal domain containing) Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

INTS12 (HGNC:25067): (integrator complex subunit 12) INTS12 is a subunit of the Integrator complex, which associates with the C-terminal domain of RNA polymerase II large subunit (POLR2A; MIM 180660) and mediates 3-prime end processing of small nuclear RNAs U1 (RNU1; MIM 180680) and U2 (RNU2; MIM 180690) (Baillat et al., 2005 [PubMed 16239144]).[supplied by OMIM, Mar 2008]

GSTCD-AS1 (HGNC:41117): (GSTCD antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0649 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GSTCD	NM_001370181.1	c.1241-9765A>G		intron_variant	Intron 5 of 11	ENST00000515279.6	NP_001357110.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GSTCD	ENST00000515279.6	c.1241-9765A>G		intron_variant	Intron 5 of 11	5	NM_001370181.1	ENSP00000422354.1
GSTCD	ENST00000394728.4	c.1241-9765A>G		intron_variant	Intron 5 of 11	5		ENSP00000378216.3

Frequencies

GnomAD3 genomes AF: 0.0539 AC: 8190 AN: 151986 Hom.: 252 Cov.: 32

Gnomad AFR AF: 0.0412

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.0686

Gnomad ASJ AF: 0.0815

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0247

Gnomad FIN AF: 0.0316

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0644

Gnomad OTH AF: 0.0765

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

GnomAD4 genome AF: 0.0538 AC: 8188 AN: 152104 Hom.: 251 Cov.: 32 AF XY: 0.0514 AC XY: 3822 AN XY: 74390

African (AFR) AF: 0.0412 AC: 1706 AN: 41422

American (AMR) AF: 0.0684 AC: 1045 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0815 AC: 283 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5192

South Asian (SAS) AF: 0.0247 AC: 119 AN: 4822

European-Finnish (FIN) AF: 0.0316 AC: 335 AN: 10610

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.0644 AC: 4375 AN: 67978

Other (OTH) AF: 0.0762 AC: 161 AN: 2114

Alfa AF: 0.0529 Hom.: 26

Bravo AF: 0.0564

Asia WGS AF: 0.0160 AC: 56 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.0
DANN	Benign	0.39
PhyloP100		0.59
Mutation Taster		=100/0	polymorphism (auto)

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: rs10516527; hg19: chr4-106734346;