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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000685067.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000288805	ENST00000685067.1		n.386-5476A>G		intron	N/A
	ENSG00000288805	ENST00000765491.1		n.411-7933A>G		intron	N/A
	ENSG00000288805	ENST00000765492.1		n.108-7933A>G		intron	N/A

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 v4.9

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;