rs6451192

Positions:

• chr5-35234227-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;