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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377171	XR_940977.4	n.216-35707C>T		intron_variant	Intron 2 of 6
LOC105377171	XR_940978.4	n.216-35707C>T		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298601	ENST00000756757.1	n.235-35707C>T		intron_variant	Intron 2 of 5
ENSG00000298601	ENST00000756759.1	n.190-35707C>T		intron_variant	Intron 2 of 5
ENSG00000298601	ENST00000756760.1	n.221-35707C>T		intron_variant	Intron 2 of 6
ENSG00000298601	ENST00000756761.1	n.235-35707C>T		intron_variant	Intron 2 of 3

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 v4.3

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

Other links and lift over

dbSNP: rs9309783; hg19: chr3-77950946;