rs4849127

Variant names:

• chr2-112844982-A-G
• rs4849127

Your query was ambiguous. Multiple possible variants found:

• chr2-112844982-A-G
• chr2-112844982-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 0.879 in 152,084 control chromosomes in the GnomAD database, including 59,347 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 0.88 (59347 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.631

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 (EAS) allele frequency at 95% confidence interval = 0.977 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: 0.879 AC: 133580 AN: 151966 Hom.: 59305 Cov.: 30

Gnomad AFR AF: 0.741

Gnomad AMI AF: 0.995

Gnomad AMR AF: 0.921

Gnomad ASJ AF: 0.871

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.859

Gnomad FIN AF: 0.930

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.937

Gnomad OTH AF: 0.879

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

GnomAD4 genome AF: 0.879 AC: 133676 AN: 152084 Hom.: 59347 Cov.: 30 AF XY: 0.880 AC XY: 65414 AN XY: 74338

Gnomad4 AFR AF: 0.741

Gnomad4 AMR AF: 0.921

Gnomad4 ASJ AF: 0.871

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.858

Gnomad4 FIN AF: 0.930

Gnomad4 NFE AF: 0.937

Gnomad4 OTH AF: 0.879

Alfa AF: 0.924 Hom.: 131678

Bravo AF: 0.874

Asia WGS AF: 0.910 AC: 3164 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	0.73
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: rs4849127; hg19: chr2-113602559;