rs1398307

Variant names:

• chr9-73627239-C-T
• rs1398307
• ENST00000715873.1:n.120-15946C>T

Variant summary

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

The ENST00000715873.1(ENSG00000232590):​n.120-15946C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 152,084 control chromosomes in the GnomAD database, including 11,944 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 0.32 (11944 hom., cov: 32)
• Consequence: ENSG00000232590 ENST00000715873.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.350
• Publications: 1 publications found

Genes affected

ENSG00000232590 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.687 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
ENSG00000232590	ENST00000715873.1	n.120-15946C>T		intron_variant	Intron 2 of 3
ENSG00000293610	ENST00000715874.1	n.355-31825G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.318 AC: 48331 AN: 151966 Hom.: 11890 Cov.: 32

Gnomad AFR AF: 0.693

Gnomad AMI AF: 0.0868

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.319 AC: 48442 AN: 152084 Hom.: 11944 Cov.: 32 AF XY: 0.313 AC XY: 23309 AN XY: 74364

African (AFR) AF: 0.694 AC: 28763 AN: 41456

American (AMR) AF: 0.277 AC: 4235 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.158 AC: 547 AN: 3472

East Asian (EAS) AF: 0.133 AC: 690 AN: 5178

South Asian (SAS) AF: 0.220 AC: 1060 AN: 4824

European-Finnish (FIN) AF: 0.159 AC: 1680 AN: 10574

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.157 AC: 10701 AN: 67976

Other (OTH) AF: 0.282 AC: 597 AN: 2114

Alfa AF: 0.203 Hom.: 19232

Bravo AF: 0.345

Asia WGS AF: 0.241 AC: 839 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.7
DANN	Benign	0.57
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs1398307; hg19: chr9-76242155;