chr4-10060702-G-A

Variant names:

• chr4-10060702-G-A
• rs6834555
• ENST00000733256.1:n.384+4778G>A

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+4778G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.74 in 152,150 control chromosomes in the GnomAD database, including 42,060 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 (42060 hom., cov: 34)
• Consequence: SLC2A9-AS1 ENST00000733256.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.609
• Publications: 23 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 = 0.777 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000733256.1. 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
	SLC2A9-AS1	ENST00000733256.1		n.384+4778G>A		intron	N/A
	SLC2A9-AS1	ENST00000733257.1		n.453+4778G>A		intron	N/A
	SLC2A9-AS1	ENST00000733258.1		n.255+4778G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.740 AC: 112473 AN: 152032 Hom.: 42035 Cov.: 34

Gnomad AFR AF: 0.753

Gnomad AMI AF: 0.652

Gnomad AMR AF: 0.602

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.524

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.772

Gnomad MID AF: 0.669

Gnomad NFE AF: 0.783

Gnomad OTH AF: 0.740

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

GnomAD4 genome AF: 0.740 AC: 112537 AN: 152150 Hom.: 42060 Cov.: 34 AF XY: 0.734 AC XY: 54590 AN XY: 74372

African (AFR) AF: 0.753 AC: 31234 AN: 41494

American (AMR) AF: 0.602 AC: 9194 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.702 AC: 2437 AN: 3472

East Asian (EAS) AF: 0.525 AC: 2719 AN: 5178

South Asian (SAS) AF: 0.662 AC: 3186 AN: 4812

European-Finnish (FIN) AF: 0.772 AC: 8159 AN: 10570

Middle Eastern (MID) AF: 0.664 AC: 194 AN: 292

European-Non Finnish (NFE) AF: 0.783 AC: 53264 AN: 68026

Other (OTH) AF: 0.737 AC: 1557 AN: 2112

Alfa AF: 0.764 Hom.: 125087

Bravo AF: 0.727

Asia WGS AF: 0.635 AC: 2213 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.35
DANN	Benign	0.36
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs6834555; hg19: chr4-10062326;