rs16879488

Variant names:

• chr4-27568088-A-G
• rs16879488

Your query was ambiguous. Multiple possible variants found:

• chr4-27568088-A-G
• chr4-27568088-A-T

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 0.0761 in 152,072 control chromosomes in the GnomAD database, including 1,157 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 0.076 (1157 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.397
• Publications: 0 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 (AFR) allele frequency at 95% confidence interval = 0.221 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: 0.0760 AC: 11554 AN: 151954 Hom.: 1152 Cov.: 32

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0343

Gnomad ASJ AF: 0.0170

Gnomad EAS AF: 0.00444

Gnomad SAS AF: 0.0917

Gnomad FIN AF: 0.0246

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0115

Gnomad OTH AF: 0.0661

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

GnomAD4 genome AF: 0.0761 AC: 11578 AN: 152072 Hom.: 1157 Cov.: 32 AF XY: 0.0754 AC XY: 5607 AN XY: 74382

African (AFR) AF: 0.225 AC: 9314 AN: 41416

American (AMR) AF: 0.0342 AC: 523 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0170 AC: 59 AN: 3472

East Asian (EAS) AF: 0.00445 AC: 23 AN: 5166

South Asian (SAS) AF: 0.0905 AC: 436 AN: 4816

European-Finnish (FIN) AF: 0.0246 AC: 261 AN: 10612

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0115 AC: 782 AN: 67988

Other (OTH) AF: 0.0716 AC: 151 AN: 2110

Alfa AF: 0.0322 Hom.: 226

Bravo AF: 0.0821

Asia WGS AF: 0.0880 AC: 304 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	0.20
DANN	Benign	0.64
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs16879488; hg19: chr4-27569710;