16-81438049-A-G

Position:

• chr16-81438049-A-G

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 0.681 in 152,028 control chromosomes in the GnomAD database, including 37,242 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 0.68 (37242 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.108

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.905 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.81438049A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.681 AC: 103412 AN: 151908 Hom.: 37186 Cov.: 31

Gnomad AFR AF: 0.913

Gnomad AMI AF: 0.437

Gnomad AMR AF: 0.658

Gnomad ASJ AF: 0.559

Gnomad EAS AF: 0.876

Gnomad SAS AF: 0.716

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.660

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

GnomAD4 genome AF: 0.681 AC: 103527 AN: 152028 Hom.: 37242 Cov.: 31 AF XY: 0.684 AC XY: 50814 AN XY: 74306

Gnomad4 AFR AF: 0.913

Gnomad4 AMR AF: 0.657

Gnomad4 ASJ AF: 0.559

Gnomad4 EAS AF: 0.875

Gnomad4 SAS AF: 0.715

Gnomad4 FIN AF: 0.586

Gnomad4 NFE AF: 0.552

Gnomad4 OTH AF: 0.663

Alfa AF: 0.569 Hom.: 30728

Bravo AF: 0.696

Asia WGS AF: 0.779 AC: 2705 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.6
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs310011; hg19: chr16-81471654;