4-99322775-T-G

Variant names:

• chr4-99322775-T-G
• rs1229982

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 0.735 in 152,062 control chromosomes in the GnomAD database, including 42,292 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 0.73 (42292 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.90
• Publications: 24 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.921 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: 0.735 AC: 111657 AN: 151946 Hom.: 42278 Cov.: 31

Gnomad AFR AF: 0.543

Gnomad AMI AF: 0.822

Gnomad AMR AF: 0.772

Gnomad ASJ AF: 0.666

Gnomad EAS AF: 0.943

Gnomad SAS AF: 0.828

Gnomad FIN AF: 0.810

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.812

Gnomad OTH AF: 0.726

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

GnomAD4 genome AF: 0.735 AC: 111702 AN: 152062 Hom.: 42292 Cov.: 31 AF XY: 0.738 AC XY: 54825 AN XY: 74318

African (AFR) AF: 0.543 AC: 22507 AN: 41458

American (AMR) AF: 0.772 AC: 11783 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.666 AC: 2314 AN: 3472

East Asian (EAS) AF: 0.943 AC: 4881 AN: 5176

South Asian (SAS) AF: 0.829 AC: 3977 AN: 4798

European-Finnish (FIN) AF: 0.810 AC: 8570 AN: 10578

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.812 AC: 55213 AN: 68000

Other (OTH) AF: 0.724 AC: 1532 AN: 2116

Alfa AF: 0.767 Hom.: 89514

Bravo AF: 0.722

Asia WGS AF: 0.835 AC: 2904 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.6
DANN	Benign	0.56
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs1229982; hg19: chr4-100243932;