rs16827671

Positions:

• chr1-150766283-T-C

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 0.359 in 151,872 control chromosomes in the GnomAD database, including 10,092 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 0.36 (10092 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0830

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.522 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: 0.359 AC: 54495 AN: 151756 Hom.: 10084 Cov.: 30

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.391

Gnomad SAS AF: 0.540

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.359 AC: 54518 AN: 151872 Hom.: 10092 Cov.: 30 AF XY: 0.364 AC XY: 27039 AN XY: 74224

Gnomad4 AFR AF: 0.292

Gnomad4 AMR AF: 0.420

Gnomad4 ASJ AF: 0.479

Gnomad4 EAS AF: 0.391

Gnomad4 SAS AF: 0.539

Gnomad4 FIN AF: 0.347

Gnomad4 NFE AF: 0.367

Gnomad4 OTH AF: 0.373

Alfa AF: 0.359 Hom.: 1626

Bravo AF: 0.354

Asia WGS AF: 0.415 AC: 1440 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.8
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16827671; hg19: chr1-150738759; COSMIC: COSV64566958;