rs16942467

Variant names:

• chr18-2033589-A-G
• rs16942467
• ENST00000584867.1:n.197-126943T>C

Variant summary

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

The ENST00000584867.1(ENSG00000263745):​n.197-126943T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 152,106 control chromosomes in the GnomAD database, including 6,933 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 0.27 (6933 hom., cov: 31)
• Consequence: ENSG00000263745 ENST00000584867.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.407
• Publications: 3 publications found

Genes affected

ENSG00000263745 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.481 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000584867.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000263745	ENST00000584867.1	TSL:2	n.197-126943T>C		intron	N/A
	ENSG00000266602	ENST00000653330.1		n.453-15398A>G		intron	N/A
	ENSG00000266602	ENST00000657750.2		n.561-15398A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.267 AC: 40559 AN: 151988 Hom.: 6909 Cov.: 31

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.267 AC: 40612 AN: 152106 Hom.: 6933 Cov.: 31 AF XY: 0.262 AC XY: 19493 AN XY: 74364

African (AFR) AF: 0.487 AC: 20190 AN: 41456

American (AMR) AF: 0.217 AC: 3321 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.209 AC: 726 AN: 3472

East Asian (EAS) AF: 0.261 AC: 1349 AN: 5166

South Asian (SAS) AF: 0.191 AC: 919 AN: 4824

European-Finnish (FIN) AF: 0.133 AC: 1407 AN: 10602

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.176 AC: 11961 AN: 67982

Other (OTH) AF: 0.267 AC: 563 AN: 2112

Alfa AF: 0.210 Hom.: 7175

Bravo AF: 0.287

Asia WGS AF: 0.250 AC: 869 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	12
DANN	Benign	0.70
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs16942467; hg19: chr18-2033590;