rs4481887

Variant names:

• chr1-248333561-A-G
• rs4481887

Your query was ambiguous. Multiple possible variants found:

• chr1-248333561-A-G
• chr1-248333561-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 0.799 in 152,170 control chromosomes in the GnomAD database, including 49,035 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 0.80 (49035 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.875 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: 0.799 AC: 121546 AN: 152052 Hom.: 48992 Cov.: 32

Gnomad AFR AF: 0.883

Gnomad AMI AF: 0.856

Gnomad AMR AF: 0.792

Gnomad ASJ AF: 0.706

Gnomad EAS AF: 0.860

Gnomad SAS AF: 0.878

Gnomad FIN AF: 0.804

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.744

Gnomad OTH AF: 0.776

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

GnomAD4 genome AF: 0.799 AC: 121647 AN: 152170 Hom.: 49035 Cov.: 32 AF XY: 0.804 AC XY: 59784 AN XY: 74404

Gnomad4 AFR AF: 0.883

Gnomad4 AMR AF: 0.791

Gnomad4 ASJ AF: 0.706

Gnomad4 EAS AF: 0.861

Gnomad4 SAS AF: 0.878

Gnomad4 FIN AF: 0.804

Gnomad4 NFE AF: 0.744

Gnomad4 OTH AF: 0.775

Alfa AF: 0.750 Hom.: 95019

Bravo AF: 0.800

Asia WGS AF: 0.864 AC: 3002 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4481887; hg19: chr1-248496863;