rs896986

chr2-44127356-G-A

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 0.513 in 152,082 control chromosomes in the GnomAD database, including 20,195 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 0.51 (20195 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.19

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.587 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: 0.513 AC: 77907 AN: 151964 Hom.: 20173 Cov.: 33

Gnomad AFR AF: 0.593

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.492

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.503

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.513 AC: 77979 AN: 152082 Hom.: 20195 Cov.: 33 AF XY: 0.511 AC XY: 37951 AN XY: 74338

Gnomad4 AFR AF: 0.593

Gnomad4 AMR AF: 0.395

Gnomad4 ASJ AF: 0.499

Gnomad4 EAS AF: 0.492

Gnomad4 SAS AF: 0.477

Gnomad4 FIN AF: 0.503

Gnomad4 NFE AF: 0.500

Gnomad4 OTH AF: 0.495

Alfa AF: 0.496 Hom.: 30503

Bravo AF: 0.508

Asia WGS AF: 0.514 AC: 1785 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.017
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs896986; hg19: chr2-44354495;