rs7684206

chr4-115793839-G-Cchr4-115793839-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.301 in 151,050 control chromosomes in the GnomAD database, including 7,120 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 0.30 (7120 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16

ACMG classification

Verdict is Benign. Variant got -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 = 0.388 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45455 AN: 150928 Hom.: 7110 Cov.: 31

Gnomad AFR AF: 0.393

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.299

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

GnomAD4 genome AF: 0.301 AC: 45493 AN: 151050 Hom.: 7120 Cov.: 31 AF XY: 0.295 AC XY: 21793 AN XY: 73766

Gnomad4 AFR AF: 0.393

Gnomad4 AMR AF: 0.234

Gnomad4 ASJ AF: 0.319

Gnomad4 EAS AF: 0.218

Gnomad4 SAS AF: 0.227

Gnomad4 FIN AF: 0.218

Gnomad4 NFE AF: 0.284

Gnomad4 OTH AF: 0.296

Alfa AF: 0.278 Hom.: 759

Bravo AF: 0.308

Asia WGS AF: 0.234 AC: 808 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.12
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7684206; hg19: chr4-116714995;