chr9-80898222-A-C

Variant names:

• chr9-80898222-A-C
• rs7025679
• ENST00000786276.1:n.194-23312A>C

Variant summary

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

The ENST00000786276.1(ENSG00000302378):​n.194-23312A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.572 in 150,730 control chromosomes in the GnomAD database, including 24,919 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 0.57 (24919 hom., cov: 28)
• Consequence: ENSG00000302378 ENST00000786276.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.380
• Publications: 1 publications found

Genes affected

ENSG00000302378 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.631 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000786276.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000302378	ENST00000786276.1		n.194-23312A>C		intron	N/A
	ENSG00000226798	ENST00000786374.1		n.80-16829T>G		intron	N/A
	ENSG00000226798	ENST00000786375.1		n.165+4543T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.572 AC: 86198 AN: 150616 Hom.: 24903 Cov.: 28

Gnomad AFR AF: 0.516

Gnomad AMI AF: 0.758

Gnomad AMR AF: 0.642

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.631

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.600

Gnomad OTH AF: 0.559

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

GnomAD4 genome AF: 0.572 AC: 86252 AN: 150730 Hom.: 24919 Cov.: 28 AF XY: 0.571 AC XY: 42040 AN XY: 73564

African (AFR) AF: 0.515 AC: 21198 AN: 41126

American (AMR) AF: 0.642 AC: 9690 AN: 15096

Ashkenazi Jewish (ASJ) AF: 0.494 AC: 1711 AN: 3464

East Asian (EAS) AF: 0.531 AC: 2649 AN: 4992

South Asian (SAS) AF: 0.401 AC: 1911 AN: 4770

European-Finnish (FIN) AF: 0.631 AC: 6563 AN: 10394

Middle Eastern (MID) AF: 0.527 AC: 154 AN: 292

European-Non Finnish (NFE) AF: 0.600 AC: 40526 AN: 67596

Other (OTH) AF: 0.555 AC: 1162 AN: 2092

Alfa AF: 0.587 Hom.: 75559

Bravo AF: 0.574

Asia WGS AF: 0.446 AC: 1551 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.30
DANN	Benign	0.45
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs7025679; hg19: chr9-83513137; COSMIC: COSV60366161;