rs1559949

Variant names:

• chr4-82419452-G-A
• rs1559949

Your query was ambiguous. Multiple possible variants found:

• chr4-82419452-G-A
• chr4-82419452-G-C

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 0.737 in 149,808 control chromosomes in the GnomAD database, including 43,673 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 0.74 (43673 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0380

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.895 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: 0.738 AC: 110415 AN: 149682 Hom.: 43658 Cov.: 26

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.649

Gnomad AMR AF: 0.811

Gnomad ASJ AF: 0.811

Gnomad EAS AF: 0.918

Gnomad SAS AF: 0.832

Gnomad FIN AF: 0.896

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.865

Gnomad OTH AF: 0.757

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

GnomAD4 genome AF: 0.737 AC: 110479 AN: 149808 Hom.: 43673 Cov.: 26 AF XY: 0.742 AC XY: 54135 AN XY: 72914

Gnomad4 AFR AF: 0.424

Gnomad4 AMR AF: 0.811

Gnomad4 ASJ AF: 0.811

Gnomad4 EAS AF: 0.917

Gnomad4 SAS AF: 0.832

Gnomad4 FIN AF: 0.896

Gnomad4 NFE AF: 0.865

Gnomad4 OTH AF: 0.758

Alfa AF: 0.837 Hom.: 77361

Bravo AF: 0.720

Asia WGS AF: 0.851 AC: 2960 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.0
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1559949; hg19: chr4-83340605;