rs7189621

chr16-62288068-A-Gchr16-62288068-A-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 0.522 in 152,002 control chromosomes in the GnomAD database, including 20,911 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 0.52 (20911 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.92

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.712 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: 0.522 AC: 79317 AN: 151884 Hom.: 20906 Cov.: 32

Gnomad AFR AF: 0.512

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.506

Gnomad EAS AF: 0.733

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.526

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

GnomAD4 genome AF: 0.522 AC: 79360 AN: 152002 Hom.: 20911 Cov.: 32 AF XY: 0.520 AC XY: 38658 AN XY: 74310

Gnomad4 AFR AF: 0.512

Gnomad4 AMR AF: 0.515

Gnomad4 ASJ AF: 0.506

Gnomad4 EAS AF: 0.732

Gnomad4 SAS AF: 0.490

Gnomad4 FIN AF: 0.479

Gnomad4 NFE AF: 0.526

Gnomad4 OTH AF: 0.521

Alfa AF: 0.519 Hom.: 26149

Bravo AF: 0.527

Asia WGS AF: 0.564 AC: 1961 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.058
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7189621; hg19: chr16-62321972;