chr4-115793839-G-C

Variant names:

• chr4-115793839-G-C
• rs7684206

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;