rs4851581

Variant names:

• chr2-102418289-A-G
• rs4851581

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 0.0625 in 152,264 control chromosomes in the GnomAD database, including 446 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 0.062 (446 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.309

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0865 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: 0.0626 AC: 9520 AN: 152146 Hom.: 446 Cov.: 33

Gnomad AFR AF: 0.0150

Gnomad AMI AF: 0.0868

Gnomad AMR AF: 0.0545

Gnomad ASJ AF: 0.0470

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0153

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0884

Gnomad OTH AF: 0.0645

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

GnomAD4 genome AF: 0.0625 AC: 9516 AN: 152264 Hom.: 446 Cov.: 33 AF XY: 0.0638 AC XY: 4747 AN XY: 74442

Gnomad4 AFR AF: 0.0149

Gnomad4 AMR AF: 0.0544

Gnomad4 ASJ AF: 0.0470

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0153

Gnomad4 FIN AF: 0.151

Gnomad4 NFE AF: 0.0884

Gnomad4 OTH AF: 0.0638

Alfa AF: 0.0733 Hom.: 79

Bravo AF: 0.0536

Asia WGS AF: 0.00837 AC: 30 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.42
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4851581; hg19: chr2-103034749;