rs30935

Variant names:

• chr16-55286589-A-G
• rs30935
• ENST00000558730.2:n.89-3925T>C

Your query was ambiguous. Multiple possible variants found:

• chr16-55286589-A-G
• chr16-55286589-A-T

Variant summary

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

The ENST00000558730.2(ENSG00000259283):​n.89-3925T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.389 in 151,930 control chromosomes in the GnomAD database, including 12,014 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 0.39 (12014 hom., cov: 32)
• Consequence: ENSG00000259283 ENST00000558730.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0990

Genes affected

ENSG00000259283 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.449 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
ENSG00000259283	ENST00000558730.2	n.89-3925T>C		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.389 AC: 59076 AN: 151812 Hom.: 12009 Cov.: 32

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.389 AC: 59103 AN: 151930 Hom.: 12014 Cov.: 32 AF XY: 0.392 AC XY: 29100 AN XY: 74286

Gnomad4 AFR AF: 0.244

Gnomad4 AMR AF: 0.458

Gnomad4 ASJ AF: 0.414

Gnomad4 EAS AF: 0.448

Gnomad4 SAS AF: 0.461

Gnomad4 FIN AF: 0.416

Gnomad4 NFE AF: 0.447

Gnomad4 OTH AF: 0.392

Alfa AF: 0.425 Hom.: 6382

Bravo AF: 0.383

Asia WGS AF: 0.426 AC: 1483 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.94
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs30935; hg19: chr16-55320501;