2-89913792-A-G

Position:

• chr2-89913792-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

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 0.022 (25 hom., cov: 19)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.673

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0217 (2116/97498) while in subpopulation AFR AF= 0.0496 (764/15410). AF 95% confidence interval is 0.0467. There are 25 homozygotes in gnomad4. There are 1063 alleles in male gnomad4 subpopulation. Median coverage is 19. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 25 gene

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: 0.0217 AC: 2116 AN: 97460 Hom.: 26 Cov.: 19

Gnomad AFR AF: 0.0496

Gnomad AMI AF: 0.00378

Gnomad AMR AF: 0.0229

Gnomad ASJ AF: 0.0103

Gnomad EAS AF: 0.0439

Gnomad SAS AF: 0.0250

Gnomad FIN AF: 0.00798

Gnomad MID AF: 0.00427

Gnomad NFE AF: 0.0153

Gnomad OTH AF: 0.0270

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

GnomAD4 genome AF: 0.0217 AC: 2116 AN: 97498 Hom.: 25 Cov.: 19 AF XY: 0.0224 AC XY: 1063 AN XY: 47456

Gnomad4 AFR AF: 0.0496

Gnomad4 AMR AF: 0.0230

Gnomad4 ASJ AF: 0.0103

Gnomad4 EAS AF: 0.0439

Gnomad4 SAS AF: 0.0240

Gnomad4 FIN AF: 0.00798

Gnomad4 NFE AF: 0.0153

Gnomad4 OTH AF: 0.0274

Alfa AF: 0.00907 Hom.: 16

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.6
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs385951; hg19: chr2-89952602;