rs12598047

Variant names:

• chr16-86019428-A-G
• rs12598047
• ENST00000838178.1:n.90+620A>G

Your query was ambiguous. Multiple possible variants found:

• chr16-86019428-A-G
• chr16-86019428-A-T

Variant summary

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

The ENST00000838178.1(ENSG00000309065):​n.90+620A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0862 in 152,304 control chromosomes in the GnomAD database, including 1,465 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 0.086 (1465 hom., cov: 33)
• Consequence: ENSG00000309065 ENST00000838178.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.830
• Publications: 3 publications found

Genes affected

ENSG00000309065 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.567 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
ENSG00000309065	ENST00000838178.1	n.90+620A>G		intron_variant	Intron 1 of 1
ENSG00000309065	ENST00000838179.1	n.83+620A>G		intron_variant	Intron 1 of 1
ENSG00000309065	ENST00000838180.1	n.82+620A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0862 AC: 13116 AN: 152186 Hom.: 1465 Cov.: 33

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0483

Gnomad ASJ AF: 0.0665

Gnomad EAS AF: 0.584

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0222

Gnomad OTH AF: 0.0764

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

GnomAD4 genome AF: 0.0862 AC: 13135 AN: 152304 Hom.: 1465 Cov.: 33 AF XY: 0.0961 AC XY: 7160 AN XY: 74482

African (AFR) AF: 0.129 AC: 5351 AN: 41564

American (AMR) AF: 0.0488 AC: 747 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.0665 AC: 231 AN: 3472

East Asian (EAS) AF: 0.584 AC: 3025 AN: 5180

South Asian (SAS) AF: 0.204 AC: 984 AN: 4828

European-Finnish (FIN) AF: 0.103 AC: 1096 AN: 10610

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0222 AC: 1513 AN: 68020

Other (OTH) AF: 0.0761 AC: 161 AN: 2116

Alfa AF: 0.0445 Hom.: 213

Bravo AF: 0.0857

Asia WGS AF: 0.342 AC: 1187 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.1
DANN	Benign	0.78
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs12598047; hg19: chr16-86053034;