rs16895984

Positions:

• chr4-10283103-C-T

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 0.605 in 151,702 control chromosomes in the GnomAD database, including 28,673 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 0.61 (28673 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.36

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.697 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: 0.605 AC: 91743 AN: 151584 Hom.: 28667 Cov.: 32

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.819

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.675

Gnomad FIN AF: 0.692

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.702

Gnomad OTH AF: 0.628

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

GnomAD4 genome AF: 0.605 AC: 91780 AN: 151702 Hom.: 28673 Cov.: 32 AF XY: 0.604 AC XY: 44811 AN XY: 74150

Gnomad4 AFR AF: 0.447

Gnomad4 AMR AF: 0.533

Gnomad4 ASJ AF: 0.591

Gnomad4 EAS AF: 0.530

Gnomad4 SAS AF: 0.675

Gnomad4 FIN AF: 0.692

Gnomad4 NFE AF: 0.702

Gnomad4 OTH AF: 0.629

Alfa AF: 0.622 Hom.: 9953

Bravo AF: 0.584

Asia WGS AF: 0.621 AC: 2161 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.85
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16895984; hg19: chr4-10284727;