rs28383797

Positions:

• chr9-21441590-G-A

Variant summary

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

The variant allele was found at a frequency of 0.0555 in 152,252 control chromosomes in the GnomAD database, including 389 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 0.055 (389 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.176 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.21441590G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR31HG	ENST00000698343.1	n.103-20898C>T		intron_variant
MIR31HG	ENST00000698344.1	n.497-20898C>T		intron_variant
MIR31HG	ENST00000698345.1	n.255-20898C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0554 AC: 8429 AN: 152134 Hom.: 387 Cov.: 31

Gnomad AFR AF: 0.0925

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.0237

Gnomad ASJ AF: 0.0493

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.0266

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0261

Gnomad OTH AF: 0.0430

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

GnomAD4 genome AF: 0.0555 AC: 8446 AN: 152252 Hom.: 389 Cov.: 31 AF XY: 0.0582 AC XY: 4336 AN XY: 74444

Gnomad4 AFR AF: 0.0927

Gnomad4 AMR AF: 0.0238

Gnomad4 ASJ AF: 0.0493

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.181

Gnomad4 FIN AF: 0.0266

Gnomad4 NFE AF: 0.0262

Gnomad4 OTH AF: 0.0440

Alfa AF: 0.0412 Hom.: 18

Bravo AF: 0.0551

Asia WGS AF: 0.150 AC: 520 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs28383797; hg19: chr9-21441589;