rs9930491

Variant names:

• chr16-22784128-G-A
• rs9930491
• ENST00000804048.1:n.313+28155C>T

Variant summary

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

The ENST00000804048.1(ENSG00000283213):​n.313+28155C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 152,160 control chromosomes in the GnomAD database, including 3,117 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 0.20 (3117 hom., cov: 32)
• Consequence: ENSG00000283213 ENST00000804048.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.511
• Publications: 4 publications found

Genes affected

ENSG00000283213 (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 (EAS) allele frequency at 95% confidence interval = 0.256 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
ENSG00000283213	ENST00000804048.1	n.313+28155C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29725 AN: 152042 Hom.: 3119 Cov.: 32

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.195 AC: 29743 AN: 152160 Hom.: 3117 Cov.: 32 AF XY: 0.194 AC XY: 14426 AN XY: 74396

African (AFR) AF: 0.237 AC: 9823 AN: 41514

American (AMR) AF: 0.143 AC: 2183 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 391 AN: 3472

East Asian (EAS) AF: 0.268 AC: 1385 AN: 5172

South Asian (SAS) AF: 0.169 AC: 815 AN: 4820

European-Finnish (FIN) AF: 0.166 AC: 1762 AN: 10602

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12669 AN: 67974

Other (OTH) AF: 0.172 AC: 362 AN: 2110

Alfa AF: 0.185 Hom.: 5223

Bravo AF: 0.195

Asia WGS AF: 0.199 AC: 693 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	2.1
DANN	Benign	0.52
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs9930491; hg19: chr16-22795449;