rs5019445

Variant names:

• chr4-181204969-A-G
• rs5019445

Your query was ambiguous. Multiple possible variants found:

• chr4-181204969-A-G
• chr4-181204969-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.731 in 151,826 control chromosomes in the GnomAD database, including 40,954 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 (40954 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.228

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.943 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: 0.731 AC: 110976 AN: 151714 Hom.: 40921 Cov.: 31

Gnomad AFR AF: 0.700

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.730

Gnomad ASJ AF: 0.680

Gnomad EAS AF: 0.966

Gnomad SAS AF: 0.878

Gnomad FIN AF: 0.828

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.697

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

GnomAD4 genome AF: 0.731 AC: 111052 AN: 151826 Hom.: 40954 Cov.: 31 AF XY: 0.739 AC XY: 54809 AN XY: 74192

Gnomad4 AFR AF: 0.699

Gnomad4 AMR AF: 0.730

Gnomad4 ASJ AF: 0.680

Gnomad4 EAS AF: 0.965

Gnomad4 SAS AF: 0.878

Gnomad4 FIN AF: 0.828

Gnomad4 NFE AF: 0.714

Gnomad4 OTH AF: 0.700

Alfa AF: 0.712 Hom.: 66332

Bravo AF: 0.718

Asia WGS AF: 0.911 AC: 3165 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.7
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5019445; hg19: chr4-182126122;