rs17802927

Variant names:

• chr16-10943881-A-G
• rs17802927

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.193 in 138,026 control chromosomes in the GnomAD database, including 2,722 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 0.19 (2722 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.210
• Publications: 15 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.226 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: 0.193 AC: 26634 AN: 137912 Hom.: 2721 Cov.: 27

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.0765

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.255

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.193 AC: 26635 AN: 138026 Hom.: 2722 Cov.: 27 AF XY: 0.192 AC XY: 12720 AN XY: 66160

African (AFR) AF: 0.120 AC: 4279 AN: 35718

American (AMR) AF: 0.182 AC: 2411 AN: 13262

Ashkenazi Jewish (ASJ) AF: 0.348 AC: 1168 AN: 3352

East Asian (EAS) AF: 0.0767 AC: 355 AN: 4630

South Asian (SAS) AF: 0.221 AC: 905 AN: 4098

European-Finnish (FIN) AF: 0.213 AC: 1832 AN: 8588

Middle Eastern (MID) AF: 0.250 AC: 70 AN: 280

European-Non Finnish (NFE) AF: 0.229 AC: 14997 AN: 65382

Other (OTH) AF: 0.217 AC: 398 AN: 1838

Alfa AF: 0.209 Hom.: 8409

Bravo AF: 0.176

Asia WGS AF: 0.152 AC: 529 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.0
DANN	Benign	0.74
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs17802927; hg19: chr16-11037738;