rs2353200

chr8-46012589-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 0.165 in 151,790 control chromosomes in the GnomAD database, including 3,943 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 0.17 (3943 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned

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 = 0.398 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: 0.165 AC: 24989 AN: 151670 Hom.: 3929 Cov.: 33

Gnomad AFR AF: 0.402

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.0816

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.0648

Gnomad MID AF: 0.0892

Gnomad NFE AF: 0.0439

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.165 AC: 25052 AN: 151790 Hom.: 3943 Cov.: 33 AF XY: 0.165 AC XY: 12215 AN XY: 74172

Gnomad4 AFR AF: 0.403

Gnomad4 AMR AF: 0.186

Gnomad4 ASJ AF: 0.0816

Gnomad4 EAS AF: 0.128

Gnomad4 SAS AF: 0.128

Gnomad4 FIN AF: 0.0648

Gnomad4 NFE AF: 0.0439

Gnomad4 OTH AF: 0.145

Alfa AF: 0.116 Hom.: 542

Bravo AF: 0.186

Asia WGS AF: 0.179 AC: 623 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	5.2
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2353200; hg19: chr8-46924211;