rs7873766

Variant names:

• chr9-32290483-T-C
• rs7873766
• ENST00000784938.1:n.705-7978A>G

Variant summary

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

The ENST00000784938.1(ENSG00000302201):​n.705-7978A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 152,190 control chromosomes in the GnomAD database, including 1,319 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 0.12 (1319 hom., cov: 32)
• Consequence: ENSG00000302201 ENST00000784938.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.283
• Publications: 3 publications found

Genes affected

ENSG00000302201 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107987059	XR_001746645.2	n.488-7978A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302201	ENST00000784938.1	n.705-7978A>G		intron_variant	Intron 2 of 2
ENSG00000302201	ENST00000784939.1	n.395-7978A>G		intron_variant	Intron 2 of 2
ENSG00000302201	ENST00000784940.1	n.197-7978A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18033 AN: 152072 Hom.: 1311 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.0967

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.0154

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0906

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.119 AC: 18056 AN: 152190 Hom.: 1319 Cov.: 32 AF XY: 0.119 AC XY: 8843 AN XY: 74414

African (AFR) AF: 0.136 AC: 5647 AN: 41518

American (AMR) AF: 0.207 AC: 3166 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 499 AN: 3472

East Asian (EAS) AF: 0.250 AC: 1289 AN: 5160

South Asian (SAS) AF: 0.147 AC: 705 AN: 4810

European-Finnish (FIN) AF: 0.0154 AC: 163 AN: 10616

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0906 AC: 6161 AN: 68010

Other (OTH) AF: 0.149 AC: 314 AN: 2112

Alfa AF: 0.108 Hom.: 195

Bravo AF: 0.134

Asia WGS AF: 0.198 AC: 688 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.1
DANN	Benign	0.84
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs7873766; hg19: chr9-32290481;