rs16985179

chr22-27633571-C-T

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 0.106 in 152,198 control chromosomes in the GnomAD database, including 940 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 0.11 (940 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.196

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.124 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: 0.106 AC: 16184 AN: 152078 Hom.: 936 Cov.: 33

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.0952

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.0679

Gnomad MID AF: 0.201

Gnomad NFE AF: 0.0970

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.106 AC: 16198 AN: 152198 Hom.: 940 Cov.: 33 AF XY: 0.107 AC XY: 7926 AN XY: 74396

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.128

Gnomad4 EAS AF: 0.0957

Gnomad4 SAS AF: 0.132

Gnomad4 FIN AF: 0.0679

Gnomad4 NFE AF: 0.0969

Gnomad4 OTH AF: 0.123

Alfa AF: 0.103 Hom.: 940

Bravo AF: 0.110

Asia WGS AF: 0.124 AC: 432 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	7.2
Dann	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16985179; hg19: chr22-28029538;