rs4849122

chr2-112803344-A-G

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 0.0364 in 152,276 control chromosomes in the GnomAD database, including 141 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 0.036 (141 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.504

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0534 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0364 AC: 5539 AN: 152158 Hom.: 141 Cov.: 32

Gnomad AFR AF: 0.00888

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.0309

Gnomad ASJ AF: 0.0613

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0155

Gnomad FIN AF: 0.0528

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0548

Gnomad OTH AF: 0.0349

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

GnomAD4 genome AF: 0.0364 AC: 5537 AN: 152276 Hom.: 141 Cov.: 32 AF XY: 0.0356 AC XY: 2651 AN XY: 74468

Gnomad4 AFR AF: 0.00883

Gnomad4 AMR AF: 0.0309

Gnomad4 ASJ AF: 0.0613

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0155

Gnomad4 FIN AF: 0.0528

Gnomad4 NFE AF: 0.0549

Gnomad4 OTH AF: 0.0345

Alfa AF: 0.0506 Hom.: 96

Bravo AF: 0.0339

Asia WGS AF: 0.00808 AC: 28 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	4.2
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4849122; hg19: chr2-113560921;