rs16828284

Variant names:

• chr1-170897037-G-A
• rs16828284
• ENST00000653116.1:n.543-32351C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000653116.1(ENSG00000231424):​n.543-32351C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0378 in 152,238 control chromosomes in the GnomAD database, including 396 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 0.038 (396 hom., cov: 32)
• Consequence: ENSG00000231424 ENST00000653116.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.497

Genes affected

ENSG00000231424 (HGNC:40240):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.127 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
ENSG00000231424	ENST00000653116.1	n.543-32351C>T		intron_variant	Intron 3 of 3
ENSG00000231424	ENST00000664920.1	n.682-89433C>T		intron_variant	Intron 4 of 5
ENSG00000231424	ENST00000669750.1	n.534-89433C>T		intron_variant	Intron 3 of 4
ENSG00000231424	ENST00000670085.1	n.372-89433C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.0377 AC: 5741 AN: 152120 Hom.: 394 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0156

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00124

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.000632

Gnomad OTH AF: 0.0320

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

GnomAD4 genome AF: 0.0378 AC: 5755 AN: 152238 Hom.: 396 Cov.: 32 AF XY: 0.0376 AC XY: 2796 AN XY: 74428

Gnomad4 AFR AF: 0.130

Gnomad4 AMR AF: 0.0155

Gnomad4 ASJ AF: 0.000288

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00104

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000632

Gnomad4 OTH AF: 0.0317

Alfa AF: 0.00736 Hom.: 68

Bravo AF: 0.0434

Asia WGS AF: 0.00837 AC: 29 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.38
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16828284; hg19: chr1-170866178;