rs2858942

Positions:

• chr16-175654-A-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;