rs4788172

Variant names:

• chr16-29656932-G-A
• rs4788172

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 0.13 in 151,968 control chromosomes in the GnomAD database, including 1,891 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 0.13 (1891 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.178

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.379 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: 0.130 AC: 19702 AN: 151850 Hom.: 1876 Cov.: 30

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.0865

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0605

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.130 AC: 19755 AN: 151968 Hom.: 1891 Cov.: 30 AF XY: 0.135 AC XY: 10018 AN XY: 74262

Gnomad4 AFR AF: 0.183

Gnomad4 AMR AF: 0.181

Gnomad4 ASJ AF: 0.112

Gnomad4 EAS AF: 0.393

Gnomad4 SAS AF: 0.329

Gnomad4 FIN AF: 0.0865

Gnomad4 NFE AF: 0.0605

Gnomad4 OTH AF: 0.136

Alfa AF: 0.0914 Hom.: 618

Bravo AF: 0.136

Asia WGS AF: 0.349 AC: 1215 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.4
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4788172; hg19: chr16-29668253;