rs7187223

chr16-82424128-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 0.0552 in 152,262 control chromosomes in the GnomAD database, including 262 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 0.055 (262 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0390

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.123 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: 0.0552 AC: 8401 AN: 152144 Hom.: 261 Cov.: 32

Gnomad AFR AF: 0.0683

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.0660

Gnomad ASJ AF: 0.0476

Gnomad EAS AF: 0.0750

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.0314

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0424

Gnomad OTH AF: 0.0550

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

GnomAD4 genome AF: 0.0552 AC: 8410 AN: 152262 Hom.: 262 Cov.: 32 AF XY: 0.0573 AC XY: 4267 AN XY: 74450

Gnomad4 AFR AF: 0.0684

Gnomad4 AMR AF: 0.0658

Gnomad4 ASJ AF: 0.0476

Gnomad4 EAS AF: 0.0755

Gnomad4 SAS AF: 0.132

Gnomad4 FIN AF: 0.0314

Gnomad4 NFE AF: 0.0424

Gnomad4 OTH AF: 0.0545

Alfa AF: 0.0464 Hom.: 181

Bravo AF: 0.0568

Asia WGS AF: 0.100 AC: 346 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.8
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7187223; hg19: chr16-82457733;