rs1522219

Variant names:

• chr4-106508345-A-C
• rs1522219

Your query was ambiguous. Multiple possible variants found:

• chr4-106508345-A-C
• chr4-106508345-A-G
• chr4-106508345-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 0.409 in 152,078 control chromosomes in the GnomAD database, including 12,825 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 0.41 (12825 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.662
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.452 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: 0.409 AC: 62108 AN: 151956 Hom.: 12807 Cov.: 32

Gnomad AFR AF: 0.438

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.409 AC: 62161 AN: 152078 Hom.: 12825 Cov.: 32 AF XY: 0.406 AC XY: 30163 AN XY: 74350

African (AFR) AF: 0.439 AC: 18185 AN: 41466

American (AMR) AF: 0.461 AC: 7038 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.403 AC: 1397 AN: 3468

East Asian (EAS) AF: 0.397 AC: 2050 AN: 5166

South Asian (SAS) AF: 0.396 AC: 1910 AN: 4826

European-Finnish (FIN) AF: 0.343 AC: 3632 AN: 10578

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.393 AC: 26739 AN: 67980

Other (OTH) AF: 0.390 AC: 822 AN: 2108

Alfa AF: 0.375 Hom.: 6601

Bravo AF: 0.420

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.88
DANN	Benign	0.59
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs1522219; hg19: chr4-107429502;