chr16-30917649-A-G

Variant names:

• chr16-30917649-A-G
• rs12924903

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 0.623 in 152,066 control chromosomes in the GnomAD database, including 30,002 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 0.62 (30002 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.505
• Publications: 41 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.884 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.623 AC: 94639 AN: 151948 Hom.: 29976 Cov.: 32

Gnomad AFR AF: 0.566

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.709

Gnomad EAS AF: 0.905

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.676

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.645

Gnomad OTH AF: 0.663

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

GnomAD4 genome AF: 0.623 AC: 94720 AN: 152066 Hom.: 30002 Cov.: 32 AF XY: 0.620 AC XY: 46081 AN XY: 74348

African (AFR) AF: 0.567 AC: 23497 AN: 41460

American (AMR) AF: 0.610 AC: 9315 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.709 AC: 2461 AN: 3472

East Asian (EAS) AF: 0.906 AC: 4692 AN: 5180

South Asian (SAS) AF: 0.317 AC: 1531 AN: 4828

European-Finnish (FIN) AF: 0.676 AC: 7143 AN: 10562

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.645 AC: 43843 AN: 67990

Other (OTH) AF: 0.660 AC: 1391 AN: 2108

Alfa AF: 0.644 Hom.: 102343

Bravo AF: 0.626

Asia WGS AF: 0.576 AC: 2009 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.8
DANN	Benign	0.27
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs12924903; hg19: chr16-30928970;