chr4-22089761-C-T

Variant names:

• chr4-22089761-C-T
• rs6448119
• ENST00000510705.3:n.723-11733C>T

Variant summary

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

The ENST00000510705.3(ENSG00000250039):​n.723-11733C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 151,948 control chromosomes in the GnomAD database, including 4,884 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 0.25 (4884 hom., cov: 32)
• Consequence: ENSG00000250039 ENST00000510705.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.686
• Publications: 7 publications found

Genes affected

ENSG00000250039 (HGNC:58742):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.356 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000510705.3. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000250039	ENST00000510705.3	TSL:5	n.723-11733C>T		intron	N/A
	ENSG00000250039	ENST00000665391.1		n.493-23663C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.253 AC: 38386 AN: 151832 Hom.: 4874 Cov.: 32

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.253 AC: 38413 AN: 151948 Hom.: 4884 Cov.: 32 AF XY: 0.252 AC XY: 18691 AN XY: 74266

African (AFR) AF: 0.272 AC: 11279 AN: 41482

American (AMR) AF: 0.271 AC: 4122 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 697 AN: 3472

East Asian (EAS) AF: 0.247 AC: 1275 AN: 5152

South Asian (SAS) AF: 0.370 AC: 1782 AN: 4818

European-Finnish (FIN) AF: 0.225 AC: 2377 AN: 10550

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.235 AC: 15993 AN: 67924

Other (OTH) AF: 0.262 AC: 553 AN: 2112

Alfa AF: 0.246 Hom.: 9099

Bravo AF: 0.255

Asia WGS AF: 0.357 AC: 1239 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.35
DANN	Benign	0.25
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs6448119; hg19: chr4-22091384;