16-67191598-C-T

Position:

• chr16-67191598-C-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 0.176 in 151,938 control chromosomes in the GnomAD database, including 4,385 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 0.18 (4385 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.921

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.67191598C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26731 AN: 151820 Hom.: 4375 Cov.: 32

Gnomad AFR AF: 0.438

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.0947

Gnomad ASJ AF: 0.0302

Gnomad EAS AF: 0.0206

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0667

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.176 AC: 26781 AN: 151938 Hom.: 4385 Cov.: 32 AF XY: 0.176 AC XY: 13082 AN XY: 74250

Gnomad4 AFR AF: 0.438

Gnomad4 AMR AF: 0.0947

Gnomad4 ASJ AF: 0.0302

Gnomad4 EAS AF: 0.0207

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.122

Gnomad4 NFE AF: 0.0667

Gnomad4 OTH AF: 0.132

Alfa AF: 0.0726 Hom.: 1233

Bravo AF: 0.183

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.7
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: rs3729639; hg19: chr16-67225501;