rs9295895

Variant names:

• chr6-30470449-T-C
• rs9295895

Your query was ambiguous. Multiple possible variants found:

• chr6-30470449-T-C
• chr6-30470449-T-G

Variant summary

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

The variant allele was found at a frequency of 0.238 in 152,156 control chromosomes in the GnomAD database, including 4,488 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 0.24 (4488 hom., cov: 32)
• Consequence: SUCLA2P1 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.573
• Publications: 26 publications found

Genes affected

SUCLA2P1 (HGNC:21632): (SUCLA2 pseudogene 1)

ENSG00000288805 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SUCLA2P1		n.30470449T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288805	ENST00000685067.1	n.386-5476A>G		intron_variant	Intron 1 of 3
ENSG00000288805	ENST00000765491.1	n.411-7933A>G		intron_variant	Intron 1 of 2
ENSG00000288805	ENST00000765492.1	n.108-7933A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36149 AN: 152036 Hom.: 4487 Cov.: 32

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.238 AC: 36162 AN: 152156 Hom.: 4488 Cov.: 32 AF XY: 0.243 AC XY: 18088 AN XY: 74412

African (AFR) AF: 0.246 AC: 10222 AN: 41500

American (AMR) AF: 0.173 AC: 2649 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.355 AC: 1231 AN: 3466

East Asian (EAS) AF: 0.433 AC: 2240 AN: 5174

South Asian (SAS) AF: 0.347 AC: 1676 AN: 4830

European-Finnish (FIN) AF: 0.269 AC: 2844 AN: 10584

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.214 AC: 14551 AN: 67986

Other (OTH) AF: 0.221 AC: 466 AN: 2112

Alfa AF: 0.221 Hom.: 13219

Bravo AF: 0.231

Asia WGS AF: 0.317 AC: 1100 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.3
DANN	Benign	0.76
PhyloP100		0.57

Splicing

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

Other links and lift over

dbSNP: rs9295895; hg19: chr6-30438226;