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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373032	XR_938256.2	n.721+9457_721+9458insTACA		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288106	ENST00000656940.1	n.172-4585_172-4584insCATA		intron_variant	Intron 1 of 1
ENSG00000288106	ENST00000717626.1	n.408+9455_408+9456insCATA		intron_variant	Intron 2 of 4
ENSG00000288106	ENST00000717627.1	n.504+1719_504+1720insCATA		intron_variant	Intron 4 of 4
ENSG00000288106	ENST00000793132.1	n.479+1719_479+1720insCATA		intron_variant	Intron 4 of 4

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 v4.3

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;