ENST00000418292.1:n.34+3668G>T

Variant names:

• chr22-28804405-G-T
• rs35679096
• ENST00000418292.1:n.34+3668G>T

Variant summary

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

The ENST00000418292.1(ENSG00000226471):​n.34+3668G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0113 in 151,880 control chromosomes in the GnomAD database, including 28 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 0.011 (28 hom., cov: 30)
• Consequence: ENSG00000226471 ENST00000418292.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171
• Publications: 2 publications found

Genes affected

ENSG00000226471 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0113 (1710/151880) while in subpopulation AFR AF = 0.0397 (1641/41384). AF 95% confidence interval is 0.0381. There are 28 homozygotes in GnomAd4. There are 788 alleles in the male GnomAd4 subpopulation. Median coverage is 30. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 28 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000418292.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000226471	ENST00000418292.1	TSL:3	n.34+3668G>T		intron	N/A
	ENSG00000226471	ENST00000451486.5	TSL:5	n.103+2411G>T		intron	N/A
	ENSG00000226471	ENST00000458080.2	TSL:3	n.55+3668G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0112 AC: 1706 AN: 151764 Hom.: 28 Cov.: 30

Gnomad AFR AF: 0.0397

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00309

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: 0.000118

Gnomad OTH AF: 0.00672

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

GnomAD4 genome AF: 0.0113 AC: 1710 AN: 151880 Hom.: 28 Cov.: 30 AF XY: 0.0106 AC XY: 788 AN XY: 74236

African (AFR) AF: 0.0397 AC: 1641 AN: 41384

American (AMR) AF: 0.00308 AC: 47 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3466

East Asian (EAS) AF: 0.00 AC: 0 AN: 5178

South Asian (SAS) AF: 0.00 AC: 0 AN: 4816

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10536

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.000118 AC: 8 AN: 67954

Other (OTH) AF: 0.00665 AC: 14 AN: 2104

Alfa AF: 0.00 Hom.: 23

Bravo AF: 0.0126

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.46
DANN	Benign	0.20
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs35679096; hg19: chr22-29200393;