rs755702

Variant names:

• chr16-64017159-A-G
• rs755702

Your query was ambiguous. Multiple possible variants found:

• chr16-64017159-A-G
• chr16-64017159-A-T

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 0.422 in 151,852 control chromosomes in the GnomAD database, including 14,180 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 0.42 (14180 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) 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: 0.422 AC: 64005 AN: 151734 Hom.: 14150 Cov.: 31

Gnomad AFR AF: 0.556

Gnomad AMI AF: 0.324

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.425

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

GnomAD4 genome AF: 0.422 AC: 64078 AN: 151852 Hom.: 14180 Cov.: 31 AF XY: 0.421 AC XY: 31229 AN XY: 74192

African (AFR) AF: 0.556 AC: 23060 AN: 41438

American (AMR) AF: 0.341 AC: 5199 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.308 AC: 1069 AN: 3466

East Asian (EAS) AF: 0.468 AC: 2395 AN: 5114

South Asian (SAS) AF: 0.443 AC: 2130 AN: 4812

European-Finnish (FIN) AF: 0.344 AC: 3631 AN: 10564

Middle Eastern (MID) AF: 0.431 AC: 125 AN: 290

European-Non Finnish (NFE) AF: 0.372 AC: 25270 AN: 67918

Other (OTH) AF: 0.429 AC: 905 AN: 2112

Alfa AF: 0.387 Hom.: 14861

Bravo AF: 0.426

Asia WGS AF: 0.453 AC: 1577 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.21
DANN	Benign	0.49
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs755702; hg19: chr16-64051063;