rs171798

Variant names:

• chr16-55710592-T-C
• rs171798

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 0.287 in 151,818 control chromosomes in the GnomAD database, including 7,817 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 0.29 (7817 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.509 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: 0.287 AC: 43489 AN: 151700 Hom.: 7797 Cov.: 32

Gnomad AFR AF: 0.515

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.276

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.287 AC: 43543 AN: 151818 Hom.: 7817 Cov.: 32 AF XY: 0.287 AC XY: 21274 AN XY: 74206

African (AFR) AF: 0.515 AC: 21315 AN: 41390

American (AMR) AF: 0.204 AC: 3114 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.253 AC: 876 AN: 3466

East Asian (EAS) AF: 0.241 AC: 1241 AN: 5150

South Asian (SAS) AF: 0.281 AC: 1352 AN: 4806

European-Finnish (FIN) AF: 0.221 AC: 2342 AN: 10584

Middle Eastern (MID) AF: 0.262 AC: 76 AN: 290

European-Non Finnish (NFE) AF: 0.183 AC: 12388 AN: 67864

Other (OTH) AF: 0.277 AC: 584 AN: 2106

Alfa AF: 0.220 Hom.: 2682

Bravo AF: 0.297

Asia WGS AF: 0.291 AC: 1013 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.7
DANN	Benign	0.83
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs171798; hg19: chr16-55744504;