rs7204293

chr16-49994194-G-Achr16-49994194-G-T

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 0.18 in 152,094 control chromosomes in the GnomAD database, including 4,339 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 0.18 (4339 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.63

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.424 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: 0.179 AC: 27279 AN: 151976 Hom.: 4326 Cov.: 32

Gnomad AFR AF: 0.429

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.0499

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.0262

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0741

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.180 AC: 27340 AN: 152094 Hom.: 4339 Cov.: 32 AF XY: 0.176 AC XY: 13086 AN XY: 74346

Gnomad4 AFR AF: 0.429

Gnomad4 AMR AF: 0.122

Gnomad4 ASJ AF: 0.0499

Gnomad4 EAS AF: 0.259

Gnomad4 SAS AF: 0.105

Gnomad4 FIN AF: 0.0262

Gnomad4 NFE AF: 0.0741

Gnomad4 OTH AF: 0.147

Alfa AF: 0.0906 Hom.: 1351

Bravo AF: 0.203

Asia WGS AF: 0.181 AC: 629 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	5.7
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7204293; hg19: chr16-50028105;