rs9309783

Variant names:

• chr3-77901795-G-A
• rs9309783
• ENST00000756757.1:n.235-35707C>T

Variant summary

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

The ENST00000756757.1(ENSG00000298601):​n.235-35707C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.626 in 151,910 control chromosomes in the GnomAD database, including 31,334 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 0.63 (31334 hom., cov: 32)
• Consequence: ENSG00000298601 ENST00000756757.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0670
• Publications: 2 publications found

Genes affected

ENSG00000298601 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.743 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000756757.1. 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
	ENSG00000298601	ENST00000756757.1		n.235-35707C>T		intron	N/A
	ENSG00000298601	ENST00000756759.1		n.190-35707C>T		intron	N/A
	ENSG00000298601	ENST00000756760.1		n.221-35707C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.626 AC: 95063 AN: 151790 Hom.: 31331 Cov.: 32

Gnomad AFR AF: 0.450

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.699

Gnomad ASJ AF: 0.718

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.748

Gnomad OTH AF: 0.651

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

GnomAD4 genome AF: 0.626 AC: 95100 AN: 151910 Hom.: 31334 Cov.: 32 AF XY: 0.616 AC XY: 45750 AN XY: 74226

African (AFR) AF: 0.450 AC: 18611 AN: 41400

American (AMR) AF: 0.700 AC: 10678 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.718 AC: 2491 AN: 3468

East Asian (EAS) AF: 0.315 AC: 1622 AN: 5154

South Asian (SAS) AF: 0.507 AC: 2440 AN: 4814

European-Finnish (FIN) AF: 0.587 AC: 6195 AN: 10550

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.748 AC: 50837 AN: 67960

Other (OTH) AF: 0.648 AC: 1362 AN: 2102

Alfa AF: 0.699 Hom.: 21046

Bravo AF: 0.628

Asia WGS AF: 0.419 AC: 1457 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.1
DANN	Benign	0.49
PhyloP100		-0.067

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9309783;

hg19: chr3-77950946;