rs16903304

Positions:

• chr5-36731123-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;