rs7098209

Variant names:

• chr10-93715713-T-C
• rs7098209
• ENST00000793614.1:n.1220-3347A>G

Variant summary

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

The ENST00000793614.1(ENSG00000303320):​n.1220-3347A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 152,128 control chromosomes in the GnomAD database, including 4,725 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 0.23 (4725 hom., cov: 32)
• Consequence: ENSG00000303320 ENST00000793614.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.649
• Publications: 5 publications found

Genes affected

ENSG00000303320 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.351 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000793614.1. 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
	ENSG00000303320	ENST00000793614.1		n.1220-3347A>G		intron	N/A
	ENSG00000303320	ENST00000793615.1		n.303-3347A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35355 AN: 152010 Hom.: 4709 Cov.: 32

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.233 AC: 35397 AN: 152128 Hom.: 4725 Cov.: 32 AF XY: 0.228 AC XY: 16993 AN XY: 74372

African (AFR) AF: 0.356 AC: 14746 AN: 41474

American (AMR) AF: 0.177 AC: 2704 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.208 AC: 720 AN: 3468

East Asian (EAS) AF: 0.275 AC: 1425 AN: 5174

South Asian (SAS) AF: 0.249 AC: 1199 AN: 4822

European-Finnish (FIN) AF: 0.142 AC: 1504 AN: 10600

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.180 AC: 12266 AN: 67988

Other (OTH) AF: 0.234 AC: 493 AN: 2106

Alfa AF: 0.201 Hom.: 9407

Bravo AF: 0.238

Asia WGS AF: 0.262 AC: 910 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.2
DANN	Benign	0.71
PhyloP100		0.65

Splicing

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

Other links and lift over

dbSNP: rs7098209; hg19: chr10-95475470;