8-16027617-T-C

Position:

• chr8-16027617-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 0.205 in 152,170 control chromosomes in the GnomAD database, including 3,616 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 0.20 (3616 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40

Genes affected

(HGNC:):

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 (SAS) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.16027617T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31143 AN: 152054 Hom.: 3620 Cov.: 33

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.0844

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.205 AC: 31149 AN: 152170 Hom.: 3616 Cov.: 33 AF XY: 0.203 AC XY: 15085 AN XY: 74394

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.182

Gnomad4 ASJ AF: 0.304

Gnomad4 EAS AF: 0.0846

Gnomad4 SAS AF: 0.270

Gnomad4 FIN AF: 0.216

Gnomad4 NFE AF: 0.266

Gnomad4 OTH AF: 0.190

Alfa AF: 0.240 Hom.: 6333

Bravo AF: 0.192

Asia WGS AF: 0.148 AC: 517 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	0.014
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8181023; hg19: chr8-15885126;