16-2274068-T-G

Variant names:

• chr16-2274068-T-G
• rs150925

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 0.543 in 152,006 control chromosomes in the GnomAD database, including 22,929 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 0.54 (22929 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.379
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.596 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: 0.543 AC: 82469 AN: 151888 Hom.: 22900 Cov.: 32

Gnomad AFR AF: 0.430

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.542

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.486

Gnomad FIN AF: 0.608

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.596

Gnomad OTH AF: 0.565

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

GnomAD4 genome AF: 0.543 AC: 82549 AN: 152006 Hom.: 22929 Cov.: 32 AF XY: 0.543 AC XY: 40373 AN XY: 74290

African (AFR) AF: 0.431 AC: 17854 AN: 41454

American (AMR) AF: 0.606 AC: 9263 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.542 AC: 1879 AN: 3468

East Asian (EAS) AF: 0.487 AC: 2510 AN: 5150

South Asian (SAS) AF: 0.488 AC: 2351 AN: 4822

European-Finnish (FIN) AF: 0.608 AC: 6432 AN: 10586

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.596 AC: 40476 AN: 67930

Other (OTH) AF: 0.562 AC: 1184 AN: 2106

Alfa AF: 0.584 Hom.: 93584

Bravo AF: 0.542

Asia WGS AF: 0.473 AC: 1646 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.0
DANN	Benign	0.33
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs150925; hg19: chr16-2324069;