16-85939006-G-A

Position:

• chr16-85939006-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000646214.1(ENSG00000285163):​n.78-6410G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 152,246 control chromosomes in the GnomAD database, including 2,992 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 0.19 (2992 hom., cov: 33)
• Consequence: ENST00000646214.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0610

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.221 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
	ENST00000646214.1	n.78-6410G>A		intron_variant, non_coding_transcript_variant
	ENST00000645383.1	n.394-6410G>A		intron_variant, non_coding_transcript_variant
	ENST00000646986.1	n.715+2995G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28687 AN: 152128 Hom.: 2992 Cov.: 33

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.0916

Gnomad EAS AF: 0.0926

Gnomad SAS AF: 0.0741

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.189 AC: 28702 AN: 152246 Hom.: 2992 Cov.: 33 AF XY: 0.187 AC XY: 13945 AN XY: 74422

Gnomad4 AFR AF: 0.134

Gnomad4 AMR AF: 0.206

Gnomad4 ASJ AF: 0.0916

Gnomad4 EAS AF: 0.0928

Gnomad4 SAS AF: 0.0744

Gnomad4 FIN AF: 0.283

Gnomad4 NFE AF: 0.224

Gnomad4 OTH AF: 0.167

Alfa AF: 0.205 Hom.: 6915

Bravo AF: 0.182

Asia WGS AF: 0.0980 AC: 341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.1
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11644034; hg19: chr16-85972612;