16-78071469-T-C

Position:

• chr16-78071469-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 0.226 in 151,974 control chromosomes in the GnomAD database, including 4,757 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 0.23 (4757 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.207

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.78071469T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34385 AN: 151856 Hom.: 4755 Cov.: 31

Gnomad AFR AF: 0.0604

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.226 AC: 34375 AN: 151974 Hom.: 4757 Cov.: 31 AF XY: 0.228 AC XY: 16933 AN XY: 74256

Gnomad4 AFR AF: 0.0603

Gnomad4 AMR AF: 0.217

Gnomad4 ASJ AF: 0.283

Gnomad4 EAS AF: 0.222

Gnomad4 SAS AF: 0.235

Gnomad4 FIN AF: 0.374

Gnomad4 NFE AF: 0.303

Gnomad4 OTH AF: 0.211

Alfa AF: 0.260 Hom.: 958

Bravo AF: 0.209

Asia WGS AF: 0.186 AC: 647 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.2
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12925573; hg19: chr16-78105366;