chr16-85847065-C-T

Position:

• chr16-85847065-C-T

Variant summary

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

The ENST00000665365.1(ENSG00000286510):​n.757C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.64 in 152,028 control chromosomes in the GnomAD database, including 33,972 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 0.64 (33972 hom., cov: 32)
• Consequence: ENST00000665365.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.34

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.792 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000665365.1	n.757C>T		non_coding_transcript_exon_variant	1/2

Frequencies

GnomAD3 genomes AF: 0.640 AC: 97242 AN: 151910 Hom.: 33977 Cov.: 32

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.905

Gnomad AMR AF: 0.545

Gnomad ASJ AF: 0.777

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.733

Gnomad FIN AF: 0.790

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.798

Gnomad OTH AF: 0.677

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

GnomAD4 genome AF: 0.640 AC: 97258 AN: 152028 Hom.: 33972 Cov.: 32 AF XY: 0.637 AC XY: 47339 AN XY: 74338

Gnomad4 AFR AF: 0.377

Gnomad4 AMR AF: 0.544

Gnomad4 ASJ AF: 0.777

Gnomad4 EAS AF: 0.388

Gnomad4 SAS AF: 0.734

Gnomad4 FIN AF: 0.790

Gnomad4 NFE AF: 0.798

Gnomad4 OTH AF: 0.680

Alfa AF: 0.731 Hom.: 11561

Bravo AF: 0.607

Asia WGS AF: 0.528 AC: 1832 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.21
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9926500; hg19: chr16-85880671;