chr16-85985481-T-A

Variant names:

• chr16-85985481-T-A
• rs13330176
• ENST00000645754.1:n.-95A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000645754.1(ENSG00000285040):​n.-95A>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.241 in 152,118 control chromosomes in the GnomAD database, including 4,878 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 0.24 (4878 hom., cov: 32)
  • Exomes 𝑓: 0.25 (0 hom.)
• Consequence: ENSG00000285040 ENST00000645754.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.375
• Publications: 48 publications found

Genes affected

ENSG00000285040 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000645754.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285040	ENST00000645754.1		n.-95A>T		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36711 AN: 151996 Hom.: 4874 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.244

GnomAD4 exome AF: 0.250 AC: 1 AN: 4 Hom.: 0 AF XY: 0.250 AC XY: 1 AN XY: 4

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AF: 0.250 AC: 1 AN: 4

GnomAD4 genome AF: 0.241 AC: 36718 AN: 152114 Hom.: 4878 Cov.: 32 AF XY: 0.242 AC XY: 18014 AN XY: 74370

African (AFR) AF: 0.205 AC: 8524 AN: 41496

American (AMR) AF: 0.382 AC: 5835 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 550 AN: 3470

East Asian (EAS) AF: 0.460 AC: 2376 AN: 5162

South Asian (SAS) AF: 0.237 AC: 1141 AN: 4820

European-Finnish (FIN) AF: 0.167 AC: 1769 AN: 10594

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.229 AC: 15551 AN: 67964

Other (OTH) AF: 0.242 AC: 511 AN: 2110

Alfa AF: 0.123 Hom.: 181

Bravo AF: 0.264

Asia WGS AF: 0.300 AC: 1042 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.6
DANN	Benign	0.61
PhyloP100		-0.38

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs13330176;

hg19: chr16-86019087;