rs16903304

Variant names:

• chr5-36731123-A-G
• rs16903304

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 0.0975 in 152,224 control chromosomes in the GnomAD database, including 768 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 (768 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00500

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0934 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: 0.0974 AC: 14819 AN: 152106 Hom.: 764 Cov.: 32

Gnomad AFR AF: 0.0907

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.0887

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.0852

Gnomad SAS AF: 0.0955

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.0954

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.0975 AC: 14848 AN: 152224 Hom.: 768 Cov.: 32 AF XY: 0.0998 AC XY: 7427 AN XY: 74428

Gnomad4 AFR AF: 0.0910

Gnomad4 AMR AF: 0.0886

Gnomad4 ASJ AF: 0.164

Gnomad4 EAS AF: 0.0848

Gnomad4 SAS AF: 0.0958

Gnomad4 FIN AF: 0.133

Gnomad4 NFE AF: 0.0954

Gnomad4 OTH AF: 0.123

Alfa AF: 0.0984 Hom.: 1478

Bravo AF: 0.0927

Asia WGS AF: 0.137 AC: 477 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	12
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16903304; hg19: chr5-36731225;