1-16169419-G-T

Variant names:

• chr1-16169419-G-T
• rs4661717

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 0.857 in 152,036 control chromosomes in the GnomAD database, including 56,299 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 0.86 (56299 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.292

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.911 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: 0.857 AC: 130145 AN: 151918 Hom.: 56258 Cov.: 30

Gnomad AFR AF: 0.730

Gnomad AMI AF: 0.948

Gnomad AMR AF: 0.911

Gnomad ASJ AF: 0.875

Gnomad EAS AF: 0.848

Gnomad SAS AF: 0.842

Gnomad FIN AF: 0.873

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.917

Gnomad OTH AF: 0.881

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

GnomAD4 genome AF: 0.857 AC: 130242 AN: 152036 Hom.: 56299 Cov.: 30 AF XY: 0.854 AC XY: 63479 AN XY: 74298

Gnomad4 AFR AF: 0.731

Gnomad4 AMR AF: 0.911

Gnomad4 ASJ AF: 0.875

Gnomad4 EAS AF: 0.849

Gnomad4 SAS AF: 0.841

Gnomad4 FIN AF: 0.873

Gnomad4 NFE AF: 0.917

Gnomad4 OTH AF: 0.882

Alfa AF: 0.875 Hom.: 5982

Bravo AF: 0.854

Asia WGS AF: 0.825 AC: 2869 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.0
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4661717; hg19: chr1-16495914;