rs7706831

Variant names:

• chr5-116723901-C-T
• rs7706831

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 0.282 in 151,958 control chromosomes in the GnomAD database, including 6,220 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 0.28 (6220 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0810

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.435 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: 0.282 AC: 42828 AN: 151840 Hom.: 6215 Cov.: 32

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.282 AC: 42863 AN: 151958 Hom.: 6220 Cov.: 32 AF XY: 0.288 AC XY: 21387 AN XY: 74246

Gnomad4 AFR AF: 0.280

Gnomad4 AMR AF: 0.281

Gnomad4 ASJ AF: 0.245

Gnomad4 EAS AF: 0.450

Gnomad4 SAS AF: 0.332

Gnomad4 FIN AF: 0.368

Gnomad4 NFE AF: 0.257

Gnomad4 OTH AF: 0.283

Alfa AF: 0.266 Hom.: 2820

Bravo AF: 0.274

Asia WGS AF: 0.355 AC: 1234 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.6
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7706831; hg19: chr5-116059597;