rs16997638

Variant names:

• chr22-37008126-A-C
• rs16997638

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 0.165 in 152,250 control chromosomes in the GnomAD database, including 2,682 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 0.17 (2682 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.787

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 (AFR) allele frequency at 95% confidence interval = 0.301 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: 0.165 AC: 25106 AN: 152132 Hom.: 2679 Cov.: 33

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.0965

Gnomad EAS AF: 0.00500

Gnomad SAS AF: 0.0855

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.165 AC: 25151 AN: 152250 Hom.: 2682 Cov.: 33 AF XY: 0.162 AC XY: 12078 AN XY: 74440

Gnomad4 AFR AF: 0.305

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.0965

Gnomad4 EAS AF: 0.00501

Gnomad4 SAS AF: 0.0860

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.110

Gnomad4 OTH AF: 0.144

Alfa AF: 0.133 Hom.: 937

Bravo AF: 0.177

Asia WGS AF: 0.0630 AC: 220 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	0.75
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16997638; hg19: chr22-37404167;