rs7800094

Variant names:

• chr7-47098118-C-A
• rs7800094
• ENST00000739919.1:n.390+3784G>T

Variant summary

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

The ENST00000739919.1(ENSG00000229192):​n.390+3784G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0579 in 152,218 control chromosomes in the GnomAD database, including 332 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 0.058 (332 hom., cov: 32)
• Consequence: ENSG00000229192 ENST00000739919.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.271
• Publications: 2 publications found

Genes affected

ENSG00000229192 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0884 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000739919.1. 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
	ENSG00000229192	ENST00000739919.1		n.390+3784G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0579 AC: 8811 AN: 152100 Hom.: 332 Cov.: 32

Gnomad AFR AF: 0.0146

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.0572

Gnomad ASJ AF: 0.0404

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0317

Gnomad FIN AF: 0.0560

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0903

Gnomad OTH AF: 0.0593

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

GnomAD4 genome AF: 0.0579 AC: 8808 AN: 152218 Hom.: 332 Cov.: 32 AF XY: 0.0551 AC XY: 4103 AN XY: 74434

African (AFR) AF: 0.0145 AC: 604 AN: 41552

American (AMR) AF: 0.0571 AC: 874 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0404 AC: 140 AN: 3466

East Asian (EAS) AF: 0.000580 AC: 3 AN: 5176

South Asian (SAS) AF: 0.0315 AC: 152 AN: 4818

European-Finnish (FIN) AF: 0.0560 AC: 594 AN: 10604

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0903 AC: 6137 AN: 67990

Other (OTH) AF: 0.0587 AC: 124 AN: 2112

Alfa AF: 0.0764 Hom.: 61

Bravo AF: 0.0563

Asia WGS AF: 0.0190 AC: 68 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.2
DANN	Benign	0.39
PhyloP100		0.27

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: rs7800094;

hg19: chr7-47137716;