rs2389803

chr4-119472356-G-A

Variant summary

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

The NR_037630.1(SEPTIN7P14):n.727+9377G>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 0.29 in 151,812 control chromosomes in the GnomAD database, including 6,464 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 0.29 (6464 hom., cov: 31)
• Consequence: SEPTIN7P14 NR_037630.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.737

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SEPTIN7P14	NR_037630.1	n.727+9377G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000688315.1	n.714+9377G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.290 AC: 43997 AN: 151694 Hom.: 6456 Cov.: 31

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.290 AC: 44041 AN: 151812 Hom.: 6464 Cov.: 31 AF XY: 0.287 AC XY: 21317 AN XY: 74200

Gnomad4 AFR AF: 0.312

Gnomad4 AMR AF: 0.273

Gnomad4 ASJ AF: 0.189

Gnomad4 EAS AF: 0.381

Gnomad4 SAS AF: 0.177

Gnomad4 FIN AF: 0.253

Gnomad4 NFE AF: 0.293

Gnomad4 OTH AF: 0.291

Alfa AF: 0.283 Hom.: 1082

Bravo AF: 0.300

Asia WGS AF: 0.257 AC: 894 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	3.3
Dann	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2389803; hg19: chr4-120393511;