rs1230165

Variant names:

• chr4-99065222-G-A
• rs1230165

Your query was ambiguous. Multiple possible variants found:

• chr4-99065222-G-A
• chr4-99065222-G-C

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 0.852 in 152,064 control chromosomes in the GnomAD database, including 55,458 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 0.85 (55458 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0630
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.971 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: 0.852 AC: 129415 AN: 151946 Hom.: 55398 Cov.: 30

Gnomad AFR AF: 0.933

Gnomad AMI AF: 0.716

Gnomad AMR AF: 0.844

Gnomad ASJ AF: 0.776

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.882

Gnomad FIN AF: 0.791

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.806

Gnomad OTH AF: 0.834

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

GnomAD4 genome AF: 0.852 AC: 129532 AN: 152064 Hom.: 55458 Cov.: 30 AF XY: 0.854 AC XY: 63470 AN XY: 74306

African (AFR) AF: 0.934 AC: 38737 AN: 41488

American (AMR) AF: 0.844 AC: 12895 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.776 AC: 2692 AN: 3470

East Asian (EAS) AF: 0.994 AC: 5137 AN: 5168

South Asian (SAS) AF: 0.882 AC: 4245 AN: 4812

European-Finnish (FIN) AF: 0.791 AC: 8347 AN: 10552

Middle Eastern (MID) AF: 0.847 AC: 249 AN: 294

European-Non Finnish (NFE) AF: 0.806 AC: 54819 AN: 67980

Other (OTH) AF: 0.836 AC: 1759 AN: 2104

Alfa AF: 0.822 Hom.: 93992

Bravo AF: 0.858

Asia WGS AF: 0.929 AC: 3229 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	7.4
DANN	Benign	0.79
PhyloP100		0.063

Splicing

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

Other links and lift over

dbSNP: rs1230165; hg19: chr4-99986373;