4-10061225-A-G

Variant names:

• chr4-10061225-A-G
• rs6820756
• ENST00000733256.1:n.384+5301A>G

Variant summary

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

The ENST00000733256.1(SLC2A9-AS1):​n.384+5301A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.741 in 152,178 control chromosomes in the GnomAD database, including 42,222 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 0.74 (42222 hom., cov: 33)
• Consequence: SLC2A9-AS1 ENST00000733256.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.08
• Publications: 6 publications found

Genes affected

SLC2A9-AS1 (HGNC:40636): (SLC2A9 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.778 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC2A9-AS1	ENST00000733256.1	n.384+5301A>G		intron_variant	Intron 3 of 3
SLC2A9-AS1	ENST00000733257.1	n.453+5301A>G		intron_variant	Intron 3 of 3
SLC2A9-AS1	ENST00000733258.1	n.255+5301A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.741 AC: 112685 AN: 152060 Hom.: 42195 Cov.: 33

Gnomad AFR AF: 0.757

Gnomad AMI AF: 0.653

Gnomad AMR AF: 0.603

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.771

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.783

Gnomad OTH AF: 0.739

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

GnomAD4 genome AF: 0.741 AC: 112752 AN: 152178 Hom.: 42222 Cov.: 33 AF XY: 0.735 AC XY: 54702 AN XY: 74402

African (AFR) AF: 0.757 AC: 31418 AN: 41514

American (AMR) AF: 0.602 AC: 9196 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.702 AC: 2436 AN: 3470

East Asian (EAS) AF: 0.526 AC: 2724 AN: 5180

South Asian (SAS) AF: 0.663 AC: 3200 AN: 4828

European-Finnish (FIN) AF: 0.771 AC: 8170 AN: 10592

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.783 AC: 53263 AN: 68004

Other (OTH) AF: 0.737 AC: 1557 AN: 2114

Alfa AF: 0.763 Hom.: 70702

Bravo AF: 0.728

Asia WGS AF: 0.636 AC: 2215 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.27
DANN	Benign	0.45
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs6820756; hg19: chr4-10062849;