rs17771897

Variant names:

• chr16-77534872-C-G
• rs17771897

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 0.0749 in 152,222 control chromosomes in the GnomAD database, including 1,245 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 0.075 (1245 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0850
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.55 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0749 AC: 11395 AN: 152104 Hom.: 1243 Cov.: 32

Gnomad AFR AF: 0.0162

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.0415

Gnomad EAS AF: 0.567

Gnomad SAS AF: 0.0414

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0566

Gnomad OTH AF: 0.0837

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

GnomAD4 genome AF: 0.0749 AC: 11401 AN: 152222 Hom.: 1245 Cov.: 32 AF XY: 0.0796 AC XY: 5920 AN XY: 74398

African (AFR) AF: 0.0162 AC: 673 AN: 41552

American (AMR) AF: 0.147 AC: 2253 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0415 AC: 144 AN: 3470

East Asian (EAS) AF: 0.567 AC: 2922 AN: 5154

South Asian (SAS) AF: 0.0413 AC: 199 AN: 4824

European-Finnish (FIN) AF: 0.106 AC: 1121 AN: 10594

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0566 AC: 3852 AN: 68018

Other (OTH) AF: 0.0842 AC: 178 AN: 2114

Alfa AF: 0.0607 Hom.: 52

Bravo AF: 0.0838

Asia WGS AF: 0.240 AC: 832 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.76
DANN	Benign	0.51
PhyloP100		0.085

Splicing

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

Other links and lift over

dbSNP: rs17771897; hg19: chr16-77568769;