rs755702

chr16-64017159-A-Gchr16-64017159-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;