rs9999446

Positions:

• chr4-73762738-A-G

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;