rs9999238

Variant names:

• chr4-104427123-A-G
• rs9999238

Your query was ambiguous. Multiple possible variants found:

• chr4-104427123-A-G
• chr4-104427123-A-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 0.724 in 151,982 control chromosomes in the GnomAD database, including 40,685 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 0.72 (40685 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.620
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.817 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: 0.724 AC: 109926 AN: 151864 Hom.: 40648 Cov.: 32

Gnomad AFR AF: 0.824

Gnomad AMI AF: 0.670

Gnomad AMR AF: 0.628

Gnomad ASJ AF: 0.805

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.646

Gnomad FIN AF: 0.692

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.720

Gnomad OTH AF: 0.735

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

GnomAD4 genome AF: 0.724 AC: 110009 AN: 151982 Hom.: 40685 Cov.: 32 AF XY: 0.717 AC XY: 53216 AN XY: 74260

African (AFR) AF: 0.825 AC: 34238 AN: 41516

American (AMR) AF: 0.628 AC: 9563 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.805 AC: 2793 AN: 3470

East Asian (EAS) AF: 0.332 AC: 1701 AN: 5128

South Asian (SAS) AF: 0.647 AC: 3113 AN: 4814

European-Finnish (FIN) AF: 0.692 AC: 7306 AN: 10562

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.720 AC: 48920 AN: 67954

Other (OTH) AF: 0.727 AC: 1532 AN: 2106

Alfa AF: 0.720 Hom.: 19130

Bravo AF: 0.724

Asia WGS AF: 0.510 AC: 1770 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.0
DANN	Benign	0.83
PhyloP100		0.62

Splicing

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

Other links and lift over

dbSNP: rs9999238; hg19: chr4-105348280;