rs16994335

chr22-34536307-G-A

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 0.151 in 151,974 control chromosomes in the GnomAD database, including 2,726 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 0.15 (2726 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

ACMG classification

Verdict is Benign. Variant got -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 = 0.327 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: 0.151 AC: 22994 AN: 151856 Hom.: 2721 Cov.: 33

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.0703

Gnomad AMR AF: 0.0736

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0291

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0897

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.151 AC: 23022 AN: 151974 Hom.: 2726 Cov.: 33 AF XY: 0.147 AC XY: 10892 AN XY: 74290

Gnomad4 AFR AF: 0.332

Gnomad4 AMR AF: 0.0734

Gnomad4 ASJ AF: 0.104

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0291

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.0897

Gnomad4 OTH AF: 0.115

Alfa AF: 0.100 Hom.: 627

Bravo AF: 0.158

Asia WGS AF: 0.0360 AC: 126 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	1.3
Dann	Benign	0.13

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16994335; hg19: chr22-34932299;