rs9999446

Variant names:

• chr4-73762738-A-G
• rs9999446

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 0.496 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.496 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

Gnomad4 AFR AF: 0.726

Gnomad4 AMR AF: 0.382

Gnomad4 ASJ AF: 0.385

Gnomad4 EAS AF: 0.391

Gnomad4 SAS AF: 0.358

Gnomad4 FIN AF: 0.370

Gnomad4 NFE AF: 0.428

Gnomad4 OTH AF: 0.474

Alfa AF: 0.431 Hom.: 20079

Bravo AF: 0.511

Asia WGS AF: 0.370 AC: 1289 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	0.077
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9999446; hg19: chr4-74628455;