chr16-82617112-A-T

Position:

• chr16-82617112-A-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 0.439 in 152,034 control chromosomes in the GnomAD database, including 15,166 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 0.44 (15166 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.291

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 = 0.486 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.82617112A>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.439 AC: 66767 AN: 151916 Hom.: 15160 Cov.: 32

Gnomad AFR AF: 0.374

Gnomad AMI AF: 0.535

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.442

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.439 AC: 66801 AN: 152034 Hom.: 15166 Cov.: 32 AF XY: 0.441 AC XY: 32795 AN XY: 74330

Gnomad4 AFR AF: 0.374

Gnomad4 AMR AF: 0.339

Gnomad4 ASJ AF: 0.421

Gnomad4 EAS AF: 0.335

Gnomad4 SAS AF: 0.441

Gnomad4 FIN AF: 0.566

Gnomad4 NFE AF: 0.490

Gnomad4 OTH AF: 0.416

Alfa AF: 0.453 Hom.: 8337

Bravo AF: 0.414

Asia WGS AF: 0.381 AC: 1325 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	2.6
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3865188; hg19: chr16-82650717;