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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.422 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

Gnomad4 AFR AF: 0.556

Gnomad4 AMR AF: 0.341

Gnomad4 ASJ AF: 0.308

Gnomad4 EAS AF: 0.468

Gnomad4 SAS AF: 0.443

Gnomad4 FIN AF: 0.344

Gnomad4 NFE AF: 0.372

Gnomad4 OTH AF: 0.429

Alfa AF: 0.381 Hom.: 11038

Bravo AF: 0.426

Asia WGS AF: 0.453 AC: 1577 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs755702; hg19: chr16-64051063;