rs40254

Variant names:

• chr16-84215151-A-G
• rs40254

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 0.743 in 152,068 control chromosomes in the GnomAD database, including 42,976 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 0.74 (42976 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.904 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: 0.743 AC: 112923 AN: 151950 Hom.: 42910 Cov.: 31

Gnomad AFR AF: 0.911

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.744

Gnomad ASJ AF: 0.650

Gnomad EAS AF: 0.743

Gnomad SAS AF: 0.733

Gnomad FIN AF: 0.769

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.645

Gnomad OTH AF: 0.744

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

GnomAD4 genome AF: 0.743 AC: 113052 AN: 152068 Hom.: 42976 Cov.: 31 AF XY: 0.749 AC XY: 55662 AN XY: 74330

African (AFR) AF: 0.912 AC: 37839 AN: 41508

American (AMR) AF: 0.744 AC: 11366 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.650 AC: 2256 AN: 3470

East Asian (EAS) AF: 0.743 AC: 3833 AN: 5156

South Asian (SAS) AF: 0.733 AC: 3522 AN: 4808

European-Finnish (FIN) AF: 0.769 AC: 8138 AN: 10588

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.645 AC: 43819 AN: 67944

Other (OTH) AF: 0.746 AC: 1572 AN: 2108

Alfa AF: 0.682 Hom.: 26613

Bravo AF: 0.747

Asia WGS AF: 0.758 AC: 2636 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.89
DANN	Benign	0.47
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs40254; hg19: chr16-84248757;