8-89198871-A-G

Variant names:

• chr8-89198871-A-G
• rs2046315

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 0.72 in 152,016 control chromosomes in the GnomAD database, including 42,391 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 0.72 (42391 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00500

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.868 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.720 AC: 109362 AN: 151898 Hom.: 42383 Cov.: 32

Gnomad AFR AF: 0.408

Gnomad AMI AF: 0.919

Gnomad AMR AF: 0.754

Gnomad ASJ AF: 0.832

Gnomad EAS AF: 0.673

Gnomad SAS AF: 0.788

Gnomad FIN AF: 0.829

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.874

Gnomad OTH AF: 0.746

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

GnomAD4 genome AF: 0.720 AC: 109402 AN: 152016 Hom.: 42391 Cov.: 32 AF XY: 0.721 AC XY: 53599 AN XY: 74296

Gnomad4 AFR AF: 0.407

Gnomad4 AMR AF: 0.754

Gnomad4 ASJ AF: 0.832

Gnomad4 EAS AF: 0.673

Gnomad4 SAS AF: 0.790

Gnomad4 FIN AF: 0.829

Gnomad4 NFE AF: 0.874

Gnomad4 OTH AF: 0.747

Alfa AF: 0.840 Hom.: 72710

Bravo AF: 0.699

Asia WGS AF: 0.691 AC: 2408 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.6
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2046315; hg19: chr8-90211100;