rs2046571

Variant names:

• chr8-121343472-G-A
• rs2046571
• ENST00000784704.1:n.162+7600G>A

Your query was ambiguous. Multiple possible variants found:

• chr8-121343472-G-A
• chr8-121343472-G-C
• chr8-121343472-G-T

Variant summary

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

The ENST00000784704.1(ENSG00000302156):​n.162+7600G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.434 in 151,884 control chromosomes in the GnomAD database, including 15,675 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 0.43 (15675 hom., cov: 32)
• Consequence: ENSG00000302156 ENST00000784704.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.185
• Publications: 10 publications found

Genes affected

ENSG00000302156 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.606 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
ENSG00000302156	ENST00000784704.1	n.162+7600G>A		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.434 AC: 65815 AN: 151766 Hom.: 15631 Cov.: 32

Gnomad AFR AF: 0.612

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.469

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.434 AC: 65913 AN: 151884 Hom.: 15675 Cov.: 32 AF XY: 0.440 AC XY: 32677 AN XY: 74224

African (AFR) AF: 0.613 AC: 25388 AN: 41432

American (AMR) AF: 0.470 AC: 7164 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.293 AC: 1015 AN: 3464

East Asian (EAS) AF: 0.583 AC: 3007 AN: 5158

South Asian (SAS) AF: 0.423 AC: 2033 AN: 4810

European-Finnish (FIN) AF: 0.443 AC: 4668 AN: 10540

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.315 AC: 21409 AN: 67918

Other (OTH) AF: 0.392 AC: 824 AN: 2102

Alfa AF: 0.345 Hom.: 17958

Bravo AF: 0.445

Asia WGS AF: 0.540 AC: 1877 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.5
DANN	Benign	0.22
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs2046571; hg19: chr8-122355712;