rs190081

Variant names:

• chr16-3273569-A-G
• rs190081
• ENST00000703449.1:c.-171+9686A>G

Variant summary

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

The ENST00000703449.1(ENSG00000290183):​c.-171+9686A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 152,156 control chromosomes in the GnomAD database, including 3,586 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 0.19 (3585 hom., cov: 31)
  • Exomes 𝑓: 0.25 (1 hom.)
• Consequence: ENSG00000290183 ENST00000703449.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.265

Genes affected

ENSG00000290183 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.282 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
ENSG00000290183	ENST00000703449.1	c.-171+9686A>G		intron_variant	Intron 1 of 1			ENSP00000515300.1
ENSG00000279330	ENST00000622989.1	n.-40A>G		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29544 AN: 152018 Hom.: 3586 Cov.: 31

Gnomad AFR AF: 0.0684

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.0377

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.208

GnomAD4 exome AF: 0.250 AC: 5 AN: 20 Hom.: 1 Cov.: 0 AF XY: 0.143 AC XY: 2 AN XY: 14

Gnomad4 EAS exome AF: 0.00

Gnomad4 NFE exome AF: 0.286

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.194 AC: 29539 AN: 152136 Hom.: 3585 Cov.: 31 AF XY: 0.196 AC XY: 14610 AN XY: 74352

Gnomad4 AFR AF: 0.0681

Gnomad4 AMR AF: 0.289

Gnomad4 ASJ AF: 0.223

Gnomad4 EAS AF: 0.0378

Gnomad4 SAS AF: 0.109

Gnomad4 FIN AF: 0.293

Gnomad4 NFE AF: 0.250

Gnomad4 OTH AF: 0.205

Alfa AF: 0.241 Hom.: 6066

Bravo AF: 0.192

Asia WGS AF: 0.0770 AC: 269 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.3
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs190081; hg19: chr16-3323569;