rs7693378

Variant names:

• chr4-69368701-C-A
• rs7693378

Variant summary

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

The variant allele was found at a frequency of 0.206 in 151,646 control chromosomes in the GnomAD database, including 3,583 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 0.21 (3583 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.193
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.296 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31148 AN: 151528 Hom.: 3574 Cov.: 29

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.206 AC: 31192 AN: 151646 Hom.: 3583 Cov.: 29 AF XY: 0.212 AC XY: 15713 AN XY: 74070

African (AFR) AF: 0.300 AC: 12428 AN: 41370

American (AMR) AF: 0.198 AC: 2998 AN: 15166

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 570 AN: 3464

East Asian (EAS) AF: 0.125 AC: 642 AN: 5146

South Asian (SAS) AF: 0.258 AC: 1240 AN: 4812

European-Finnish (FIN) AF: 0.282 AC: 2957 AN: 10502

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.143 AC: 9717 AN: 67872

Other (OTH) AF: 0.197 AC: 416 AN: 2110

Alfa AF: 0.162 Hom.: 5448

Bravo AF: 0.203

Asia WGS AF: 0.217 AC: 757 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.0
DANN	Benign	0.25
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs7693378; hg19: chr4-70234419;