rs75560005

Variant names:

• chr6-29636005-T-C
• rs75560005
• ENST00000782059.1:n.621A>G

Variant summary

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

The ENST00000782059.1(ENSG00000301820):​n.621A>G 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 0.00629 in 1,478,756 control chromosomes in the GnomAD database, including 272 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 0.0060 (18 hom., cov: 32)
  • Exomes 𝑓: 0.0063 (254 hom.)
• Consequence: ENSG00000301820 ENST00000782059.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.548
• Publications: 0 publications found

Genes affected

ENSG00000301820 (HGNC:):

SUMO2P1 (HGNC:13985): (SUMO2 pseudogene 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0631 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SUMO2P1		n.29636005T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301820	ENST00000782059.1	n.621A>G		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000301820	ENST00000782060.1	n.617A>G		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000301820	ENST00000782061.1	n.497A>G		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.00598 AC: 911 AN: 152214 Hom.: 18 Cov.: 32

Gnomad AFR AF: 0.000700

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.00209

Gnomad ASJ AF: 0.00432

Gnomad EAS AF: 0.0693

Gnomad SAS AF: 0.0549

Gnomad FIN AF: 0.000942

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00263

Gnomad OTH AF: 0.00621

GnomAD4 exome AF: 0.00633 AC: 8396 AN: 1326424 Hom.: 254 AF XY: 0.00776 AC XY: 5172 AN XY: 666300

African (AFR) AF: 0.000587 AC: 18 AN: 30676

American (AMR) AF: 0.00169 AC: 72 AN: 42640

Ashkenazi Jewish (ASJ) AF: 0.00484 AC: 122 AN: 25216

East Asian (EAS) AF: 0.0472 AC: 1833 AN: 38866

South Asian (SAS) AF: 0.0491 AC: 4075 AN: 83030

European-Finnish (FIN) AF: 0.00158 AC: 71 AN: 44992

Middle Eastern (MID) AF: 0.0128 AC: 57 AN: 4436

European-Non Finnish (NFE) AF: 0.00168 AC: 1679 AN: 1000402

Other (OTH) AF: 0.00835 AC: 469 AN: 56166

GnomAD4 genome AF: 0.00597 AC: 909 AN: 152332 Hom.: 18 Cov.: 32 AF XY: 0.00726 AC XY: 541 AN XY: 74488

African (AFR) AF: 0.000698 AC: 29 AN: 41576

American (AMR) AF: 0.00209 AC: 32 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.00432 AC: 15 AN: 3472

East Asian (EAS) AF: 0.0690 AC: 358 AN: 5186

South Asian (SAS) AF: 0.0550 AC: 265 AN: 4820

European-Finnish (FIN) AF: 0.000942 AC: 10 AN: 10620

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.00263 AC: 179 AN: 68034

Other (OTH) AF: 0.00615 AC: 13 AN: 2114

Alfa AF: 0.00344 Hom.: 0

Bravo AF: 0.00550

Asia WGS AF: 0.0540 AC: 187 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	7.6
DANN	Benign	0.55
PhyloP100		0.55

Splicing

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

Other links and lift over

dbSNP: rs75560005; hg19: chr6-29603782;