rs922028

Variant names:

• chr4-179866601-A-G
• rs922028

Your query was ambiguous. Multiple possible variants found:

• chr4-179866601-A-G
• chr4-179866601-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 0.202 in 152,114 control chromosomes in the GnomAD database, including 3,276 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 0.20 (3276 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.450
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.229 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: 0.202 AC: 30748 AN: 151996 Hom.: 3274 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.0684

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.202 AC: 30751 AN: 152114 Hom.: 3276 Cov.: 32 AF XY: 0.198 AC XY: 14753 AN XY: 74374

African (AFR) AF: 0.171 AC: 7099 AN: 41492

American (AMR) AF: 0.168 AC: 2564 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 1226 AN: 3468

East Asian (EAS) AF: 0.0682 AC: 353 AN: 5176

South Asian (SAS) AF: 0.145 AC: 699 AN: 4826

European-Finnish (FIN) AF: 0.201 AC: 2127 AN: 10574

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.232 AC: 15774 AN: 67968

Other (OTH) AF: 0.232 AC: 490 AN: 2114

Alfa AF: 0.217 Hom.: 2348

Bravo AF: 0.200

Asia WGS AF: 0.122 AC: 425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.2
DANN	Benign	0.46
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs922028; hg19: chr4-180787754;