4-105842654-A-T

Variant names:

• chr4-105842654-A-T
• rs7676975
• NM_001370181.1:c.1765+520A>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.1765+520A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 152,250 control chromosomes in the GnomAD database, including 1,408 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 0.11 (1408 hom., cov: 32)
• Consequence: GSTCD NM_001370181.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.582
• Publications: 3 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=-0.64).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.219 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.1765+520A>T		intron	N/A	NP_001357110.1	Q8NEC7-1
	GSTCD	NM_001031720.3		c.1765+520A>T		intron	N/A	NP_001026890.2	Q8NEC7-1
	GSTCD	NM_024751.3		c.1504+520A>T		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.1765+520A>T		intron	N/A	ENSP00000422354.1	Q8NEC7-1
	GSTCD	ENST00000360505.9	TSL:1	c.1765+520A>T		intron	N/A	ENSP00000353695.5	Q8NEC7-1
	GSTCD	ENST00000394728.4	TSL:5	c.1765+520A>T		intron	N/A	ENSP00000378216.3	Q8NEC7-1

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16613 AN: 152130 Hom.: 1395 Cov.: 32

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.0977

Gnomad ASJ AF: 0.0824

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0254

Gnomad FIN AF: 0.0318

Gnomad MID AF: 0.166

Gnomad NFE AF: 0.0694

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.109 AC: 16665 AN: 152250 Hom.: 1408 Cov.: 32 AF XY: 0.105 AC XY: 7825 AN XY: 74458

African (AFR) AF: 0.223 AC: 9254 AN: 41500

American (AMR) AF: 0.0974 AC: 1491 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0824 AC: 286 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5190

South Asian (SAS) AF: 0.0255 AC: 123 AN: 4832

European-Finnish (FIN) AF: 0.0318 AC: 338 AN: 10616

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.0694 AC: 4722 AN: 68020

Other (OTH) AF: 0.132 AC: 278 AN: 2112

Alfa AF: 0.0812 Hom.: 92

Bravo AF: 0.120

Asia WGS AF: 0.0310 AC: 108 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	12
DANN	Benign	0.88
PhyloP100		0.58
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: rs7676975; hg19: chr4-106763811;