1-22247449-T-C

Variant names:

• chr1-22247449-T-C
• rs909814
• ENST00000725701.1:n.412-25357T>C

Variant summary

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

The ENST00000725701.1(ENSG00000294752):​n.412-25357T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.592 in 152,114 control chromosomes in the GnomAD database, including 27,255 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 0.59 (27255 hom., cov: 33)
• Consequence: ENSG00000294752 ENST00000725701.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0150
• Publications: 13 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.785 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.412-25357T>C		intron_variant	Intron 3 of 3
ENSG00000294752	ENST00000725702.1	n.236-25357T>C		intron_variant	Intron 2 of 2
ENSG00000294752	ENST00000725703.1	n.393+17369T>C		intron_variant	Intron 3 of 3
ENSG00000294752	ENST00000725704.1	n.215-25357T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.592 AC: 90036 AN: 151996 Hom.: 27243 Cov.: 33

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.708

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.805

Gnomad SAS AF: 0.627

Gnomad FIN AF: 0.695

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.616

Gnomad OTH AF: 0.580

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

GnomAD4 genome AF: 0.592 AC: 90100 AN: 152114 Hom.: 27255 Cov.: 33 AF XY: 0.599 AC XY: 44563 AN XY: 74370

African (AFR) AF: 0.481 AC: 19951 AN: 41474

American (AMR) AF: 0.629 AC: 9624 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.597 AC: 2072 AN: 3470

East Asian (EAS) AF: 0.805 AC: 4166 AN: 5174

South Asian (SAS) AF: 0.628 AC: 3028 AN: 4820

European-Finnish (FIN) AF: 0.695 AC: 7364 AN: 10600

Middle Eastern (MID) AF: 0.486 AC: 141 AN: 290

European-Non Finnish (NFE) AF: 0.616 AC: 41871 AN: 67960

Other (OTH) AF: 0.586 AC: 1237 AN: 2112

Alfa AF: 0.601 Hom.: 43852

Bravo AF: 0.581

Asia WGS AF: 0.732 AC: 2542 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.2
DANN	Benign	0.44
PhyloP100		-0.015

Splicing

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

Other links and lift over

dbSNP: rs909814; hg19: chr1-22573942;