rs16874223

Variant names:

• chr6-13562045-G-T
• rs16874223

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 0.0726 in 152,082 control chromosomes in the GnomAD database, including 514 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 0.073 (514 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.346

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.127 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: 0.0724 AC: 10995 AN: 151966 Hom.: 502 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.0297

Gnomad EAS AF: 0.0264

Gnomad SAS AF: 0.0532

Gnomad FIN AF: 0.0419

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0496

Gnomad OTH AF: 0.0707

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

GnomAD4 genome AF: 0.0726 AC: 11043 AN: 152082 Hom.: 514 Cov.: 32 AF XY: 0.0730 AC XY: 5429 AN XY: 74334

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.132

Gnomad4 ASJ AF: 0.0297

Gnomad4 EAS AF: 0.0264

Gnomad4 SAS AF: 0.0537

Gnomad4 FIN AF: 0.0419

Gnomad4 NFE AF: 0.0496

Gnomad4 OTH AF: 0.0700

Alfa AF: 0.0583 Hom.: 443

Bravo AF: 0.0825

Asia WGS AF: 0.0490 AC: 173 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.0
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16874223; hg19: chr6-13562277;