ENST00000665365.1:n.757C>T

Variant names:

• chr16-85847065-C-T
• rs9926500
• ENST00000665365.1:n.757C>T

Variant summary

Our verdict is Benign. The variant received -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: ENSG00000286510 ENST00000665365.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.34
• Publications: 2 publications found

Genes affected

ENSG00000286510 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286510	ENST00000665365.1	n.757C>T		non_coding_transcript_exon_variant	Exon 1 of 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

African (AFR) AF: 0.377 AC: 15628 AN: 41438

American (AMR) AF: 0.544 AC: 8314 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.777 AC: 2694 AN: 3468

East Asian (EAS) AF: 0.388 AC: 2002 AN: 5164

South Asian (SAS) AF: 0.734 AC: 3528 AN: 4808

European-Finnish (FIN) AF: 0.790 AC: 8356 AN: 10574

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.798 AC: 54230 AN: 67982

Other (OTH) AF: 0.680 AC: 1434 AN: 2110

Alfa AF: 0.716 Hom.: 17860

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
PhyloP100		-3.3

Splicing

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

Other links and lift over

dbSNP: rs9926500; hg19: chr16-85880671;