rs16879418

Variant names:

• chr5-7914519-C-T
• rs16879418

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 0.264 in 152,138 control chromosomes in the GnomAD database, including 5,493 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 0.26 (5493 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.442
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.289 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: 0.265 AC: 40222 AN: 152020 Hom.: 5495 Cov.: 32

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.264 AC: 40230 AN: 152138 Hom.: 5493 Cov.: 32 AF XY: 0.265 AC XY: 19709 AN XY: 74364

African (AFR) AF: 0.234 AC: 9733 AN: 41522

American (AMR) AF: 0.213 AC: 3258 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.217 AC: 755 AN: 3472

East Asian (EAS) AF: 0.188 AC: 972 AN: 5182

South Asian (SAS) AF: 0.239 AC: 1151 AN: 4818

European-Finnish (FIN) AF: 0.338 AC: 3573 AN: 10572

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.293 AC: 19895 AN: 67980

Other (OTH) AF: 0.250 AC: 529 AN: 2114

Alfa AF: 0.277 Hom.: 5491

Bravo AF: 0.252

Asia WGS AF: 0.173 AC: 605 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.5
DANN	Benign	0.60
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs16879418; hg19: chr5-7914632;