rs1399431

Variant names:

• chr9-117895628-G-A
• rs1399431
• ENST00000449730.1:n.74+1555C>T

Variant summary

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

The ENST00000449730.1(ENSG00000231901):​n.74+1555C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.42 in 151,862 control chromosomes in the GnomAD database, including 13,439 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 0.42 (13439 hom., cov: 32)
• Consequence: ENSG00000231901 ENST00000449730.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.110

Genes affected

ENSG00000231901 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.487 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
ENSG00000231901	ENST00000449730.1	n.74+1555C>T		intron_variant	Intron 1 of 3	3
ENSG00000285082	ENST00000665764.1	n.*16+47473G>A		intron_variant	Intron 2 of 6			ENSP00000499745.1
ENSG00000285082	ENST00000697636.1	n.*16+47473G>A		intron_variant	Intron 2 of 5			ENSP00000513366.1

Frequencies

GnomAD3 genomes AF: 0.420 AC: 63659 AN: 151742 Hom.: 13424 Cov.: 32

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.464

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.420 AC: 63709 AN: 151862 Hom.: 13439 Cov.: 32 AF XY: 0.419 AC XY: 31091 AN XY: 74196

Gnomad4 AFR AF: 0.411

Gnomad4 AMR AF: 0.496

Gnomad4 ASJ AF: 0.464

Gnomad4 EAS AF: 0.305

Gnomad4 SAS AF: 0.307

Gnomad4 FIN AF: 0.393

Gnomad4 NFE AF: 0.426

Gnomad4 OTH AF: 0.440

Alfa AF: 0.421 Hom.: 1678

Bravo AF: 0.427

Asia WGS AF: 0.302 AC: 1050 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.69
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1399431; hg19: chr9-120657906;