rs1398829

Positions:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000510705.3(ENSG00000250039):​n.446-37432T>A variant causes a intron, non coding transcript 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: ENST00000510705.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.583

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000510705.3	n.446-37432T>A		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.424

Gnomad4 AMR AF: 0.926

Gnomad4 ASJ AF: 0.958

Gnomad4 EAS AF: 0.930

Gnomad4 SAS AF: 0.954

Gnomad4 FIN AF: 0.998

Gnomad4 NFE AF: 0.984

Gnomad4 OTH AF: 0.869

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1398829; hg19: chr4-22023275;