16-1081695-A-G

Position:

• chr16-1081695-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 0.62 in 151,914 control chromosomes in the GnomAD database, including 30,144 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 0.62 (30144 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.943

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.620 AC: 94113 AN: 151796 Hom.: 30113 Cov.: 32

Gnomad AFR AF: 0.700

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.637

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.653

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.618

Gnomad OTH AF: 0.607

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

GnomAD4 genome AF: 0.620 AC: 94192 AN: 151914 Hom.: 30144 Cov.: 32 AF XY: 0.618 AC XY: 45862 AN XY: 74252

Gnomad4 AFR AF: 0.700

Gnomad4 AMR AF: 0.638

Gnomad4 ASJ AF: 0.473

Gnomad4 EAS AF: 0.135

Gnomad4 SAS AF: 0.493

Gnomad4 FIN AF: 0.653

Gnomad4 NFE AF: 0.618

Gnomad4 OTH AF: 0.600

Alfa AF: 0.598 Hom.: 14182

Bravo AF: 0.623

Asia WGS AF: 0.326 AC: 1138 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.7
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs197056; hg19: chr16-1131695; COSMIC: COSV53513622;