16-62288068-A-G

Variant names:

• chr16-62288068-A-G
• rs7189621

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.512 AC: 21232 AN: 41446

American (AMR) AF: 0.515 AC: 7859 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.506 AC: 1756 AN: 3472

East Asian (EAS) AF: 0.732 AC: 3780 AN: 5166

South Asian (SAS) AF: 0.490 AC: 2361 AN: 4820

European-Finnish (FIN) AF: 0.479 AC: 5056 AN: 10566

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.526 AC: 35768 AN: 67958

Other (OTH) AF: 0.521 AC: 1096 AN: 2104

Alfa AF: 0.519 Hom.: 33528

Bravo AF: 0.527

Asia WGS AF: 0.564 AC: 1961 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.058
DANN	Benign	0.64
PhyloP100		-3.9

Splicing

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

Other links and lift over

dbSNP: rs7189621; hg19: chr16-62321972;