rs6436122

chr2-219171668-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 0.864 in 152,208 control chromosomes in the GnomAD database, including 57,946 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 0.86 (57946 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.954 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: 0.864 AC: 131442 AN: 152090 Hom.: 57925 Cov.: 32

Gnomad AFR AF: 0.745

Gnomad AMI AF: 0.944

Gnomad AMR AF: 0.810

Gnomad ASJ AF: 0.964

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.846

Gnomad FIN AF: 0.946

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.960

Gnomad OTH AF: 0.873

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

GnomAD4 genome AF: 0.864 AC: 131515 AN: 152208 Hom.: 57946 Cov.: 32 AF XY: 0.859 AC XY: 63917 AN XY: 74418

Gnomad4 AFR AF: 0.745

Gnomad4 AMR AF: 0.810

Gnomad4 ASJ AF: 0.964

Gnomad4 EAS AF: 0.482

Gnomad4 SAS AF: 0.846

Gnomad4 FIN AF: 0.946

Gnomad4 NFE AF: 0.960

Gnomad4 OTH AF: 0.867

Alfa AF: 0.936 Hom.: 132324

Bravo AF: 0.845

Asia WGS AF: 0.647 AC: 2254 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.017
Dann	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6436122; hg19: chr2-220036390;