2-90038664-A-G

Position:

• chr2-90038664-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 0.906 in 150,372 control chromosomes in the GnomAD database, including 62,241 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 0.91 (62241 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.278

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.932 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.90038664A>G		intergenic_region
IGK		n.90038664A>G		intragenic_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.906 AC: 136124 AN: 150252 Hom.: 62171 Cov.: 31

Gnomad AFR AF: 0.940

Gnomad AMI AF: 0.902

Gnomad AMR AF: 0.918

Gnomad ASJ AF: 0.845

Gnomad EAS AF: 0.934

Gnomad SAS AF: 0.911

Gnomad FIN AF: 0.921

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.883

Gnomad OTH AF: 0.884

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

GnomAD4 genome AF: 0.906 AC: 136256 AN: 150372 Hom.: 62241 Cov.: 31 AF XY: 0.908 AC XY: 66684 AN XY: 73406

Gnomad4 AFR AF: 0.940

Gnomad4 AMR AF: 0.918

Gnomad4 ASJ AF: 0.845

Gnomad4 EAS AF: 0.934

Gnomad4 SAS AF: 0.912

Gnomad4 FIN AF: 0.921

Gnomad4 NFE AF: 0.883

Gnomad4 OTH AF: 0.885

Alfa AF: 0.910 Hom.: 28414

Bravo AF: 0.908

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.64
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2847840; hg19: chr2-90077496;