rs1398829

Variant names:

• chr4-22021652-T-A
• rs1398829
• ENST00000510705.3:n.446-37432T>A

Your query was ambiguous. Multiple possible variants found:

• chr4-22021652-T-A
• chr4-22021652-T-G

Variant summary

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

The ENST00000510705.3(ENSG00000250039):​n.446-37432T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.822 in 152,218 control chromosomes in the GnomAD database, including 56,081 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 0.82 (56081 hom., cov: 33)
• Consequence: ENSG00000250039 ENST00000510705.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.583
• Publications: 6 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.978 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000250039	ENST00000510705.3	TSL:5	n.446-37432T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.822 AC: 125025 AN: 152100 Hom.: 56075 Cov.: 33

Gnomad AFR AF: 0.424

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.926

Gnomad ASJ AF: 0.958

Gnomad EAS AF: 0.930

Gnomad SAS AF: 0.954

Gnomad FIN AF: 0.998

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.984

Gnomad OTH AF: 0.868

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

GnomAD4 genome AF: 0.822 AC: 125071 AN: 152218 Hom.: 56081 Cov.: 33 AF XY: 0.827 AC XY: 61589 AN XY: 74438

African (AFR) AF: 0.424 AC: 17558 AN: 41448

American (AMR) AF: 0.926 AC: 14171 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.958 AC: 3327 AN: 3472

East Asian (EAS) AF: 0.930 AC: 4818 AN: 5180

South Asian (SAS) AF: 0.954 AC: 4607 AN: 4830

European-Finnish (FIN) AF: 0.998 AC: 10606 AN: 10628

Middle Eastern (MID) AF: 0.912 AC: 268 AN: 294

European-Non Finnish (NFE) AF: 0.984 AC: 66970 AN: 68042

Other (OTH) AF: 0.869 AC: 1834 AN: 2110

Alfa AF: 0.889 Hom.: 7873

Bravo AF: 0.800

Asia WGS AF: 0.921 AC: 3204 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.3
DANN	Benign	0.47
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs1398829; hg19: chr4-22023275;