rs150925

Positions:

• chr16-2274068-T-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 0.543 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.431

Gnomad4 AMR AF: 0.606

Gnomad4 ASJ AF: 0.542

Gnomad4 EAS AF: 0.487

Gnomad4 SAS AF: 0.488

Gnomad4 FIN AF: 0.608

Gnomad4 NFE AF: 0.596

Gnomad4 OTH AF: 0.562

Alfa AF: 0.557 Hom.: 2313

Bravo AF: 0.542

Asia WGS AF: 0.473 AC: 1646 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs150925; hg19: chr16-2324069;