chr1-22204641-C-T

Variant names:

• chr1-22204641-C-T
• rs926435
• ENST00000725701.1:n.411+15706C>T

Variant summary

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

The ENST00000725701.1(ENSG00000294752):​n.411+15706C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0637 in 152,228 control chromosomes in the GnomAD database, including 438 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 0.064 (438 hom., cov: 33)
• Consequence: ENSG00000294752 ENST00000725701.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.896
• Publications: 4 publications found

Genes affected

ENSG00000294752 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0943 is higher than 0.05.

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
ENSG00000294752	ENST00000725701.1	n.411+15706C>T		intron_variant	Intron 3 of 3
ENSG00000294752	ENST00000725702.1	n.235+15706C>T		intron_variant	Intron 2 of 2
ENSG00000294752	ENST00000725703.1	n.218+15706C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.0639 AC: 9713 AN: 152110 Hom.: 439 Cov.: 33

Gnomad AFR AF: 0.0173

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.0695

Gnomad ASJ AF: 0.0903

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0307

Gnomad FIN AF: 0.0631

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0963

Gnomad OTH AF: 0.0793

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

GnomAD4 genome AF: 0.0637 AC: 9703 AN: 152228 Hom.: 438 Cov.: 33 AF XY: 0.0615 AC XY: 4578 AN XY: 74428

African (AFR) AF: 0.0173 AC: 718 AN: 41564

American (AMR) AF: 0.0695 AC: 1062 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0903 AC: 313 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5170

South Asian (SAS) AF: 0.0303 AC: 146 AN: 4818

European-Finnish (FIN) AF: 0.0631 AC: 669 AN: 10596

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0962 AC: 6544 AN: 68000

Other (OTH) AF: 0.0780 AC: 165 AN: 2116

Alfa AF: 0.0750 Hom.: 66

Bravo AF: 0.0615

Asia WGS AF: 0.0150 AC: 52 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	15
DANN	Benign	0.79
PhyloP100		0.90

Splicing

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

Other links and lift over

dbSNP: rs926435; hg19: chr1-22531134;