rs2042360

Variant names:

• chr16-64123913-T-C
• rs2042360
• ENST00000720938.1:n.-26T>C

Variant summary

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

The ENST00000720938.1(ENSG00000294094):​n.-26T>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 152,128 control chromosomes in the GnomAD database, including 2,879 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 0.18 (2879 hom., cov: 32)
• Consequence: ENSG00000294094 ENST00000720938.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0610
• Publications: 5 publications found

Genes affected

ENSG00000294094 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.332 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000720938.1. 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
	ENSG00000294094	ENST00000720938.1		n.-26T>C		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27110 AN: 152010 Hom.: 2871 Cov.: 32

Gnomad AFR AF: 0.0693

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.178 AC: 27133 AN: 152128 Hom.: 2879 Cov.: 32 AF XY: 0.180 AC XY: 13422 AN XY: 74364

African (AFR) AF: 0.0693 AC: 2880 AN: 41538

American (AMR) AF: 0.199 AC: 3033 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.214 AC: 742 AN: 3468

East Asian (EAS) AF: 0.257 AC: 1323 AN: 5150

South Asian (SAS) AF: 0.346 AC: 1668 AN: 4822

European-Finnish (FIN) AF: 0.158 AC: 1675 AN: 10582

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.221 AC: 15057 AN: 67988

Other (OTH) AF: 0.210 AC: 443 AN: 2114

Alfa AF: 0.213 Hom.: 2399

Bravo AF: 0.175

Asia WGS AF: 0.302 AC: 1047 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.86
DANN	Benign	0.69
PhyloP100		-0.061

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: rs2042360;

hg19: chr16-64157817;