rs9378540

Variant names:

• chr6-8335142-A-G
• rs9378540
• ENST00000439891.3:n.956+5219A>G

Variant summary

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

The ENST00000439891.3(ENSG00000232234):​n.956+5219A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.288 in 152,122 control chromosomes in the GnomAD database, including 6,631 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 (6631 hom., cov: 32)
• Consequence: ENSG00000232234 ENST00000439891.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0180

Genes affected

ENSG00000232234 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.314 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
ENSG00000232234	ENST00000439891.3	n.956+5219A>G		intron_variant	Intron 6 of 6	5
ENSG00000232234	ENST00000642149.1	n.586-7183A>G		intron_variant	Intron 5 of 5
ENSG00000232234	ENST00000643735.1	n.736+6865A>G		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43745 AN: 152004 Hom.: 6617 Cov.: 32

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.0378

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.288 AC: 43786 AN: 152122 Hom.: 6631 Cov.: 32 AF XY: 0.279 AC XY: 20775 AN XY: 74372

Gnomad4 AFR AF: 0.318

Gnomad4 AMR AF: 0.269

Gnomad4 ASJ AF: 0.371

Gnomad4 EAS AF: 0.0380

Gnomad4 SAS AF: 0.307

Gnomad4 FIN AF: 0.168

Gnomad4 NFE AF: 0.303

Gnomad4 OTH AF: 0.326

Alfa AF: 0.286 Hom.: 1021

Bravo AF: 0.298

Asia WGS AF: 0.179 AC: 623 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9378540; hg19: chr6-8335375;