rs9999446

Variant names:

• chr4-73762738-A-G
• rs9999446

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 0.496 in 152,004 control chromosomes in the GnomAD database, including 20,228 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 0.50 (20228 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.91
• Publications: 10 publications found

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 (AFR) allele frequency at 95% confidence interval = 0.719 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.496 AC: 75388 AN: 151886 Hom.: 20200 Cov.: 31

Gnomad AFR AF: 0.725

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.496 AC: 75465 AN: 152004 Hom.: 20228 Cov.: 31 AF XY: 0.488 AC XY: 36234 AN XY: 74302

African (AFR) AF: 0.726 AC: 30055 AN: 41422

American (AMR) AF: 0.382 AC: 5839 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.385 AC: 1336 AN: 3468

East Asian (EAS) AF: 0.391 AC: 2018 AN: 5158

South Asian (SAS) AF: 0.358 AC: 1728 AN: 4824

European-Finnish (FIN) AF: 0.370 AC: 3913 AN: 10568

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.428 AC: 29090 AN: 67978

Other (OTH) AF: 0.474 AC: 1002 AN: 2112

Alfa AF: 0.449 Hom.: 53900

Bravo AF: 0.511

Asia WGS AF: 0.370 AC: 1289 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.077
DANN	Benign	0.28
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs9999446; hg19: chr4-74628455; COSMIC: COSV107199629;