rs16895984

Variant names:

• chr4-10283103-C-T
• rs16895984

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 0.605 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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.447 AC: 18450 AN: 41306

American (AMR) AF: 0.533 AC: 8120 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.591 AC: 2047 AN: 3464

East Asian (EAS) AF: 0.530 AC: 2714 AN: 5120

South Asian (SAS) AF: 0.675 AC: 3241 AN: 4804

European-Finnish (FIN) AF: 0.692 AC: 7320 AN: 10578

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.702 AC: 47653 AN: 67874

Other (OTH) AF: 0.629 AC: 1327 AN: 2110

Alfa AF: 0.586 Hom.: 16730

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
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs16895984; hg19: chr4-10284727;