rs2055729

Positions:

• chr8-9935152-G-A
• chr8-9935152-G-C

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 0.548 in 151,962 control chromosomes in the GnomAD database, including 24,910 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 0.55 (24910 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.138

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.663 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.548 AC: 83243 AN: 151848 Hom.: 24901 Cov.: 31

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.727

Gnomad AMR AF: 0.637

Gnomad ASJ AF: 0.732

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.673

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.668

Gnomad OTH AF: 0.617

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

GnomAD4 genome AF: 0.548 AC: 83255 AN: 151962 Hom.: 24910 Cov.: 31 AF XY: 0.547 AC XY: 40659 AN XY: 74274

Gnomad4 AFR AF: 0.299

Gnomad4 AMR AF: 0.638

Gnomad4 ASJ AF: 0.732

Gnomad4 EAS AF: 0.390

Gnomad4 SAS AF: 0.674

Gnomad4 FIN AF: 0.544

Gnomad4 NFE AF: 0.668

Gnomad4 OTH AF: 0.609

Alfa AF: 0.641 Hom.: 27251

Bravo AF: 0.539

Asia WGS AF: 0.511 AC: 1776 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.42
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2055729; hg19: chr8-9792662;