rs6451192

Variant names:

• chr5-35234227-A-G
• rs6451192

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 0.139 in 152,148 control chromosomes in the GnomAD database, including 2,642 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 0.14 (2642 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.206

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.331 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: 0.139 AC: 21165 AN: 152030 Hom.: 2633 Cov.: 31

Gnomad AFR AF: 0.335

Gnomad AMI AF: 0.0440

Gnomad AMR AF: 0.0712

Gnomad ASJ AF: 0.0744

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.0228

Gnomad FIN AF: 0.0998

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0557

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.139 AC: 21204 AN: 152148 Hom.: 2642 Cov.: 31 AF XY: 0.138 AC XY: 10285 AN XY: 74400

Gnomad4 AFR AF: 0.335

Gnomad4 AMR AF: 0.0717

Gnomad4 ASJ AF: 0.0744

Gnomad4 EAS AF: 0.131

Gnomad4 SAS AF: 0.0232

Gnomad4 FIN AF: 0.0998

Gnomad4 NFE AF: 0.0556

Gnomad4 OTH AF: 0.120

Alfa AF: 0.109 Hom.: 274

Bravo AF: 0.147

Asia WGS AF: 0.0910 AC: 316 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.5
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: rs6451192; hg19: chr5-35234329;