chr16-16622120-T-A

Variant names:

• chr16-16622120-T-A
• rs4430769
• ENST00000567465.2:n.88-26224T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000567465.2(ENSG00000260126):​n.88-26224T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00897 in 149,490 control chromosomes in the GnomAD database, including 39 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 0.0090 (39 hom., cov: 29)
• Consequence: ENSG00000260126 ENST00000567465.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.278
• Publications: 3 publications found

Genes affected

ENSG00000260126 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00897 (1341/149490) while in subpopulation AFR AF = 0.0318 (1293/40690). AF 95% confidence interval is 0.0303. There are 39 homozygotes in GnomAd4. There are 630 alleles in the male GnomAd4 subpopulation. Median coverage is 29. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 39 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000260126	ENST00000567465.2	n.88-26224T>A		intron_variant	Intron 1 of 4	3
ENSG00000287905	ENST00000660246.1	n.156+9587T>A		intron_variant	Intron 1 of 1
ENSG00000260126	ENST00000840420.1	n.82-26224T>A		intron_variant	Intron 1 of 3
ENSG00000287905	ENST00000840523.1	n.54+8407T>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.00898 AC: 1341 AN: 149376 Hom.: 39 Cov.: 29

Gnomad AFR AF: 0.0319

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00200

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000592

Gnomad OTH AF: 0.00691

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

GnomAD4 genome AF: 0.00897 AC: 1341 AN: 149490 Hom.: 39 Cov.: 29 AF XY: 0.00864 AC XY: 630 AN XY: 72890

African (AFR) AF: 0.0318 AC: 1293 AN: 40690

American (AMR) AF: 0.00200 AC: 30 AN: 15020

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3430

East Asian (EAS) AF: 0.00 AC: 0 AN: 4484

South Asian (SAS) AF: 0.00 AC: 0 AN: 4612

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10446

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 292

European-Non Finnish (NFE) AF: 0.0000592 AC: 4 AN: 67564

Other (OTH) AF: 0.00686 AC: 14 AN: 2040

Alfa AF: 0.00735 Hom.: 7

Bravo AF: 0.0109

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.8
DANN	Benign	0.74
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs4430769; hg19: chr16-16715977;