rs2320289

Variant names:

• chr4-18160481-A-C
• rs2320289
• ENST00000796675.1:n.293+598A>C

Your query was ambiguous. Multiple possible variants found:

• chr4-18160481-A-C
• chr4-18160481-A-G

Variant summary

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

The ENST00000796675.1(ENSG00000303707):​n.293+598A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 152,126 control chromosomes in the GnomAD database, including 3,629 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 0.21 (3629 hom., cov: 33)
• Consequence: ENSG00000303707 ENST00000796675.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.288
• Publications: 6 publications found

Genes affected

ENSG00000303707 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.468 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
ENSG00000303707	ENST00000796675.1	n.293+598A>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32044 AN: 152008 Hom.: 3611 Cov.: 33

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.485

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.211 AC: 32081 AN: 152126 Hom.: 3629 Cov.: 33 AF XY: 0.214 AC XY: 15935 AN XY: 74376

African (AFR) AF: 0.204 AC: 8480 AN: 41502

American (AMR) AF: 0.281 AC: 4291 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.157 AC: 544 AN: 3464

East Asian (EAS) AF: 0.484 AC: 2498 AN: 5158

South Asian (SAS) AF: 0.172 AC: 829 AN: 4824

European-Finnish (FIN) AF: 0.174 AC: 1847 AN: 10592

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.189 AC: 12831 AN: 67992

Other (OTH) AF: 0.229 AC: 482 AN: 2108

Alfa AF: 0.197 Hom.: 4409

Bravo AF: 0.222

Asia WGS AF: 0.350 AC: 1216 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	2.8
DANN	Benign	0.52
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs2320289; hg19: chr4-18162104;