rs11726124

Variant names:

• chr4-105845339-A-G
• rs11726124
• NM_001370181.1:c.1766-102A>G

Your query was ambiguous. Multiple possible variants found:

• chr4-105845339-A-G
• chr4-105845339-A-T

Variant summary

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

The NM_001370181.1(GSTCD):​c.1766-102A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0603 in 1,250,050 control chromosomes in the GnomAD database, including 2,539 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 0.055 (258 hom., cov: 32)
  • Exomes 𝑓: 0.061 (2281 hom.)
• Consequence: GSTCD NM_001370181.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.217
• Publications: 8 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0651 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001370181.1. 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
	GSTCD	NM_001370181.1	MANE Select	c.1766-102A>G		intron	N/A	NP_001357110.1	Q8NEC7-1
	GSTCD	NM_001031720.3		c.1766-102A>G		intron	N/A	NP_001026890.2	Q8NEC7-1
	GSTCD	NM_024751.3		c.1505-102A>G		intron	N/A	NP_079027.2	Q8NEC7-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GSTCD	ENST00000515279.6	TSL:5 MANE Select	c.1766-102A>G		intron	N/A	ENSP00000422354.1	Q8NEC7-1
	GSTCD	ENST00000360505.9	TSL:1	c.1766-102A>G		intron	N/A	ENSP00000353695.5	Q8NEC7-1
	GSTCD	ENST00000394728.4	TSL:5	c.1766-102A>G		intron	N/A	ENSP00000378216.3	Q8NEC7-1

Frequencies

GnomAD3 genomes AF: 0.0550 AC: 8373 AN: 152212 Hom.: 259 Cov.: 32

Gnomad AFR AF: 0.0422

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.0687

Gnomad ASJ AF: 0.0815

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0248

Gnomad FIN AF: 0.0316

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0662

Gnomad OTH AF: 0.0770

GnomAD4 exome AF: 0.0610 AC: 66985 AN: 1097720 Hom.: 2281 AF XY: 0.0602 AC XY: 33353 AN XY: 554466

African (AFR) AF: 0.0444 AC: 1176 AN: 26506

American (AMR) AF: 0.0463 AC: 1924 AN: 41514

Ashkenazi Jewish (ASJ) AF: 0.0811 AC: 1741 AN: 21462

East Asian (EAS) AF: 0.000318 AC: 12 AN: 37686

South Asian (SAS) AF: 0.0349 AC: 2481 AN: 71040

European-Finnish (FIN) AF: 0.0383 AC: 1809 AN: 47234

Middle Eastern (MID) AF: 0.0930 AC: 462 AN: 4970

European-Non Finnish (NFE) AF: 0.0681 AC: 54437 AN: 799186

Other (OTH) AF: 0.0612 AC: 2943 AN: 48122

GnomAD4 genome AF: 0.0550 AC: 8371 AN: 152330 Hom.: 258 Cov.: 32 AF XY: 0.0525 AC XY: 3914 AN XY: 74502

African (AFR) AF: 0.0422 AC: 1754 AN: 41572

American (AMR) AF: 0.0685 AC: 1048 AN: 15300

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

East Asian (EAS) AF: 0.00 AC: 0 AN: 5190

South Asian (SAS) AF: 0.0249 AC: 120 AN: 4826

European-Finnish (FIN) AF: 0.0316 AC: 336 AN: 10624

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

European-Non Finnish (NFE) AF: 0.0662 AC: 4505 AN: 68028

Other (OTH) AF: 0.0766 AC: 162 AN: 2114

Alfa AF: 0.0539 Hom.: 45

Bravo AF: 0.0577

Asia WGS AF: 0.0160 AC: 57 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.2
DANN	Benign	0.67
PhyloP100		0.22
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: rs11726124; hg19: chr4-106766496;