rs16852397

Variant names:

• chr1-178061466-A-G
• rs16852397
• ENST00000784499.1:n.188+2901A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000784499.1(ENSG00000302121):​n.188+2901A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0625 in 152,226 control chromosomes in the GnomAD database, including 369 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 0.063 (369 hom., cov: 32)
• Consequence: ENSG00000302121 ENST00000784499.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07
• Publications: 5 publications found

Genes affected

ENSG00000302121 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0789 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
ENSG00000302121	ENST00000784499.1	n.188+2901A>G		intron_variant	Intron 1 of 2
ENSG00000302121	ENST00000784500.1	n.86+2901A>G		intron_variant	Intron 1 of 3
ENSG00000302121	ENST00000784501.1	n.38+2901A>G		intron_variant	Intron 1 of 3
ENSG00000302121	ENST00000784502.1	n.390+1680A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0625 AC: 9514 AN: 152108 Hom.: 369 Cov.: 32

Gnomad AFR AF: 0.0299

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.0828

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.0517

Gnomad SAS AF: 0.0732

Gnomad FIN AF: 0.0518

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0749

Gnomad OTH AF: 0.0915

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

GnomAD4 genome AF: 0.0625 AC: 9519 AN: 152226 Hom.: 369 Cov.: 32 AF XY: 0.0627 AC XY: 4667 AN XY: 74406

African (AFR) AF: 0.0300 AC: 1246 AN: 41556

American (AMR) AF: 0.0827 AC: 1265 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 402 AN: 3472

East Asian (EAS) AF: 0.0518 AC: 268 AN: 5170

South Asian (SAS) AF: 0.0730 AC: 352 AN: 4820

European-Finnish (FIN) AF: 0.0518 AC: 549 AN: 10598

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.0749 AC: 5096 AN: 67996

Other (OTH) AF: 0.0905 AC: 191 AN: 2110

Alfa AF: 0.0629 Hom.: 56

Bravo AF: 0.0637

Asia WGS AF: 0.0440 AC: 154 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
CADD	Benign	16
DANN	Benign	0.84
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs16852397; hg19: chr1-178030601;