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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000782059.1. 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
	ENSG00000301820	ENST00000782059.1		n.621A>G		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000301820	ENST00000782060.1		n.617A>G		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000301820	ENST00000782061.1		n.497A>G		non_coding_transcript_exon	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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs75560005;

hg19: chr6-29603782;