rs1659127

Variant names:

• chr16-14294448-G-A
• rs1659127

Your query was ambiguous. Multiple possible variants found:

• chr16-14294448-G-A
• chr16-14294448-G-C
• chr16-14294448-G-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 0.328 in 151,992 control chromosomes in the GnomAD database, including 8,441 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 0.33 (8441 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0950

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.521 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: 0.329 AC: 49909 AN: 151874 Hom.: 8438 Cov.: 32

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.539

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.312

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.328 AC: 49926 AN: 151992 Hom.: 8441 Cov.: 32 AF XY: 0.329 AC XY: 24462 AN XY: 74296

Gnomad4 AFR AF: 0.299

Gnomad4 AMR AF: 0.311

Gnomad4 ASJ AF: 0.262

Gnomad4 EAS AF: 0.538

Gnomad4 SAS AF: 0.307

Gnomad4 FIN AF: 0.335

Gnomad4 NFE AF: 0.338

Gnomad4 OTH AF: 0.361

Alfa AF: 0.331 Hom.: 10111

Bravo AF: 0.325

Asia WGS AF: 0.417 AC: 1452 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.0
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1659127; hg19: chr16-14388305;