rs16890720

Variant names:

• chr6-79422575-G-A
• rs16890720
• ENST00000654165.1:n.1898G>A

Variant summary

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

The ENST00000654165.1(ENSG00000231533):​n.1898G>A 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 0.174 in 151,976 control chromosomes in the GnomAD database, including 2,609 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 0.17 (2609 hom., cov: 32)
• Consequence: ENSG00000231533 ENST00000654165.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.361
• Publications: 7 publications found

Genes affected

ENSG00000231533 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000654165.1. 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
	ENSG00000231533	ENST00000654165.1		n.1898G>A		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000231533	ENST00000652956.1		n.184+372G>A		intron	N/A
	ENSG00000231533	ENST00000653204.1		n.526+1387G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26368 AN: 151858 Hom.: 2612 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.100

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.0687

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.174 AC: 26376 AN: 151976 Hom.: 2609 Cov.: 32 AF XY: 0.168 AC XY: 12461 AN XY: 74332

African (AFR) AF: 0.267 AC: 11082 AN: 41448

American (AMR) AF: 0.149 AC: 2270 AN: 15262

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

East Asian (EAS) AF: 0.100 AC: 518 AN: 5176

South Asian (SAS) AF: 0.135 AC: 650 AN: 4820

European-Finnish (FIN) AF: 0.0687 AC: 729 AN: 10606

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.146 AC: 9921 AN: 67884

Other (OTH) AF: 0.180 AC: 380 AN: 2106

Alfa AF: 0.166 Hom.: 2496

Bravo AF: 0.186

Asia WGS AF: 0.125 AC: 438 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.0
DANN	Benign	0.39
PhyloP100		-0.36

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: rs16890720;

hg19: chr6-80132292;