rs2858942

Variant names:

• chr16-175654-A-C
• rs2858942

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 0.752 in 147,994 control chromosomes in the GnomAD database, including 43,348 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 0.75 (43348 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.921 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: 0.751 AC: 111126 AN: 147876 Hom.: 43287 Cov.: 30

Gnomad AFR AF: 0.929

Gnomad AMI AF: 0.782

Gnomad AMR AF: 0.703

Gnomad ASJ AF: 0.727

Gnomad EAS AF: 0.514

Gnomad SAS AF: 0.701

Gnomad FIN AF: 0.661

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.700

Gnomad OTH AF: 0.711

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

GnomAD4 genome AF: 0.752 AC: 111249 AN: 147994 Hom.: 43348 Cov.: 30 AF XY: 0.746 AC XY: 53966 AN XY: 72344

Gnomad4 AFR AF: 0.929

Gnomad4 AMR AF: 0.703

Gnomad4 ASJ AF: 0.727

Gnomad4 EAS AF: 0.514

Gnomad4 SAS AF: 0.702

Gnomad4 FIN AF: 0.661

Gnomad4 NFE AF: 0.700

Gnomad4 OTH AF: 0.715

Alfa AF: 0.714 Hom.: 41874

Bravo AF: 0.767

Asia WGS AF: 0.663 AC: 2176 AN: 3286

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	1.0
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2858942; hg19: chr16-225653;