rs16843298

Variant names:

• chr1-198549416-C-A
• rs16843298

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 0.0976 in 152,100 control chromosomes in the GnomAD database, including 1,017 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 0.098 (1017 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.184 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: 0.0977 AC: 14846 AN: 151982 Hom.: 1016 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.0716

Gnomad AMR AF: 0.0616

Gnomad ASJ AF: 0.0984

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0394

Gnomad FIN AF: 0.0435

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0719

Gnomad OTH AF: 0.0924

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

GnomAD4 genome AF: 0.0976 AC: 14850 AN: 152100 Hom.: 1017 Cov.: 32 AF XY: 0.0938 AC XY: 6976 AN XY: 74356

African (AFR) AF: 0.187 AC: 7753 AN: 41460

American (AMR) AF: 0.0615 AC: 940 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0984 AC: 341 AN: 3466

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5182

South Asian (SAS) AF: 0.0390 AC: 188 AN: 4818

European-Finnish (FIN) AF: 0.0435 AC: 460 AN: 10580

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0718 AC: 4884 AN: 67992

Other (OTH) AF: 0.0910 AC: 192 AN: 2110

Alfa AF: 0.0885 Hom.: 119

Bravo AF: 0.104

Asia WGS AF: 0.0310 AC: 107 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.056
DANN	Benign	0.43
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs16843298; hg19: chr1-198518546; COSMIC: COSV60015643;