rs378411

Variant names:

• chr6-52940006-A-G
• rs378411
• ENST00000406231.1:n.511T>C

Variant summary

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

The ENST00000406231.1(GSTA9P):​n.511T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 152,116 control chromosomes in the GnomAD database, including 3,363 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 0.19 (3361 hom., cov: 32)
  • Exomes 𝑓: 0.55 (2 hom.)
• Consequence: GSTA9P ENST00000406231.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.215
• Publications: 2 publications found

Genes affected

GSTA9P (HGNC:49902): (glutathione S-transferase alpha 9, pseudogene)

ENSG00000291036 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GSTA9P		n.52940006A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GSTA9P	ENST00000406231.1	n.511T>C		non_coding_transcript_exon_variant	Exon 6 of 6	6
ENSG00000291036	ENST00000448991.7	n.509T>C		non_coding_transcript_exon_variant	Exon 6 of 6	3
ENSG00000291036	ENST00000763228.1	n.486T>C		non_coding_transcript_exon_variant	Exon 5 of 5

Frequencies

GnomAD3 genomes AF: 0.190 AC: 28845 AN: 151978 Hom.: 3357 Cov.: 32

Gnomad AFR AF: 0.0810

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.0421

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.217

GnomAD4 exome AF: 0.550 AC: 11 AN: 20 Hom.: 2 Cov.: 0 AF XY: 0.333 AC XY: 2 AN XY: 6

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 8 AN: 16

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 2 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.190 AC: 28849 AN: 152096 Hom.: 3361 Cov.: 32 AF XY: 0.186 AC XY: 13800 AN XY: 74320

African (AFR) AF: 0.0810 AC: 3364 AN: 41506

American (AMR) AF: 0.200 AC: 3048 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.256 AC: 889 AN: 3472

East Asian (EAS) AF: 0.0412 AC: 213 AN: 5164

South Asian (SAS) AF: 0.127 AC: 612 AN: 4816

European-Finnish (FIN) AF: 0.218 AC: 2298 AN: 10564

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.261 AC: 17717 AN: 67984

Other (OTH) AF: 0.216 AC: 456 AN: 2114

Alfa AF: 0.241 Hom.: 2813

Bravo AF: 0.183

Asia WGS AF: 0.0790 AC: 276 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	17
DANN	Benign	0.81
PhyloP100		0.21

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs378411; hg19: chr6-52804804;