rs17781622

Variant names:

• chr16-87580359-A-G
• rs17781622

Your query was ambiguous. Multiple possible variants found:

• chr16-87580359-A-G
• chr16-87580359-A-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 0.175 in 150,234 control chromosomes in the GnomAD database, including 2,789 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 0.18 (2789 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.332

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 (EAS) allele frequency at 95% confidence interval = 0.384 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: 0.175 AC: 26265 AN: 150126 Hom.: 2772 Cov.: 29

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.175 AC: 26326 AN: 150234 Hom.: 2789 Cov.: 29 AF XY: 0.182 AC XY: 13327 AN XY: 73118

Gnomad4 AFR AF: 0.196

Gnomad4 AMR AF: 0.293

Gnomad4 ASJ AF: 0.139

Gnomad4 EAS AF: 0.398

Gnomad4 SAS AF: 0.176

Gnomad4 FIN AF: 0.165

Gnomad4 NFE AF: 0.124

Gnomad4 OTH AF: 0.179

Alfa AF: 0.159 Hom.: 304

Bravo AF: 0.192

Asia WGS AF: 0.261 AC: 903 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.2
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17781622; hg19: chr16-87613965;