rs9990270

Variant names:

• chr3-190458817-C-G
• rs9990270

Your query was ambiguous. Multiple possible variants found:

• chr3-190458817-C-G
• chr3-190458817-C-T

Variant summary

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

The variant allele was found at a frequency of 0.569 in 151,652 control chromosomes in the GnomAD database, including 25,112 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 0.57 (25112 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.274
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.635 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

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86216 AN: 151534 Hom.: 25094 Cov.: 31

Gnomad AFR AF: 0.641

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.571

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.431

Gnomad FIN AF: 0.550

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.583

Gnomad OTH AF: 0.568

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

GnomAD4 genome AF: 0.569 AC: 86276 AN: 151652 Hom.: 25112 Cov.: 31 AF XY: 0.561 AC XY: 41603 AN XY: 74124

African (AFR) AF: 0.641 AC: 26576 AN: 41436

American (AMR) AF: 0.460 AC: 6992 AN: 15184

Ashkenazi Jewish (ASJ) AF: 0.571 AC: 1980 AN: 3468

East Asian (EAS) AF: 0.303 AC: 1560 AN: 5154

South Asian (SAS) AF: 0.433 AC: 2083 AN: 4812

European-Finnish (FIN) AF: 0.550 AC: 5764 AN: 10486

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.583 AC: 39547 AN: 67800

Other (OTH) AF: 0.562 AC: 1185 AN: 2108

Alfa AF: 0.452 Hom.: 1243

Bravo AF: 0.565

Asia WGS AF: 0.406 AC: 1397 AN: 3442

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.3
DANN	Benign	0.33
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs9990270; hg19: chr3-190176606;