rs16394

Variant names:

• chr22-38896462-T-TCATA
• rs16394
• ENST00000656940.1:n.172-4585_172-4584insCATA

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000656940.1(ENSG00000288106):​n.172-4585_172-4584insCATA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.70 (38978 hom., cov: 0)
• Consequence: ENSG00000288106 ENST00000656940.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.62
• Publications: 2 publications found

Genes affected

ENSG00000288106 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.915 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000656940.1. 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
	ENSG00000288106	ENST00000656940.1		n.172-4585_172-4584insCATA		intron	N/A
	ENSG00000288106	ENST00000717626.1		n.408+9455_408+9456insCATA		intron	N/A
	ENSG00000288106	ENST00000717627.1		n.504+1719_504+1720insCATA		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.704 AC: 105792 AN: 150274 Hom.: 38936 Cov.: 0

Gnomad AFR AF: 0.923

Gnomad AMI AF: 0.731

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.630

Gnomad EAS AF: 0.842

Gnomad SAS AF: 0.679

Gnomad FIN AF: 0.603

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.623

Gnomad OTH AF: 0.676

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

GnomAD4 genome AF: 0.704 AC: 105875 AN: 150378 Hom.: 38978 Cov.: 0 AF XY: 0.701 AC XY: 51358 AN XY: 73310

African (AFR) AF: 0.923 AC: 37837 AN: 40982

American (AMR) AF: 0.522 AC: 7865 AN: 15070

Ashkenazi Jewish (ASJ) AF: 0.630 AC: 2185 AN: 3468

East Asian (EAS) AF: 0.841 AC: 4313 AN: 5126

South Asian (SAS) AF: 0.678 AC: 3240 AN: 4782

European-Finnish (FIN) AF: 0.603 AC: 5999 AN: 9950

Middle Eastern (MID) AF: 0.684 AC: 197 AN: 288

European-Non Finnish (NFE) AF: 0.623 AC: 42165 AN: 67718

Other (OTH) AF: 0.676 AC: 1413 AN: 2090

Alfa AF: 0.481 Hom.: 805

Asia WGS AF: 0.745 AC: 2575 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs16394; hg19: chr22-39292467;