rs4849127

Positions:

• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;