rs9325872

Variant names:

• chr8-20622760-A-G
• rs9325872
• ENST00000778369.1:n.214-42074A>G

Variant summary

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

The ENST00000778369.1(ENSG00000301347):​n.214-42074A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.482 in 151,768 control chromosomes in the GnomAD database, including 20,693 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 0.48 (20693 hom., cov: 30)
• Consequence: ENSG00000301347 ENST00000778369.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00400
• Publications: 10 publications found

Genes affected

ENSG00000301347 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.647 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
ENSG00000301347	ENST00000778369.1	n.214-42074A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.482 AC: 73121 AN: 151650 Hom.: 20694 Cov.: 30

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.665

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.637

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.627

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.652

Gnomad OTH AF: 0.504

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

GnomAD4 genome AF: 0.482 AC: 73122 AN: 151768 Hom.: 20693 Cov.: 30 AF XY: 0.479 AC XY: 35486 AN XY: 74152

African (AFR) AF: 0.226 AC: 9360 AN: 41392

American (AMR) AF: 0.396 AC: 6028 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.637 AC: 2209 AN: 3468

East Asian (EAS) AF: 0.103 AC: 531 AN: 5138

South Asian (SAS) AF: 0.471 AC: 2258 AN: 4796

European-Finnish (FIN) AF: 0.627 AC: 6603 AN: 10528

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.652 AC: 44301 AN: 67904

Other (OTH) AF: 0.503 AC: 1058 AN: 2104

Alfa AF: 0.585 Hom.: 117745

Bravo AF: 0.448

Asia WGS AF: 0.290 AC: 1013 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.8
DANN	Benign	0.31
PhyloP100		0.0040

Splicing

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

Other links and lift over

dbSNP: rs9325872; hg19: chr8-20480271;