rs6946733

Variant names:

• chr7-107029843-G-A
• rs6946733

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 0.263 in 152,092 control chromosomes in the GnomAD database, including 6,453 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 0.26 (6453 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.320

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.409 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: 0.263 AC: 39998 AN: 151976 Hom.: 6463 Cov.: 32

Gnomad AFR AF: 0.0671

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.365

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.263 AC: 39986 AN: 152092 Hom.: 6453 Cov.: 32 AF XY: 0.272 AC XY: 20216 AN XY: 74332

Gnomad4 AFR AF: 0.0669

Gnomad4 AMR AF: 0.380

Gnomad4 ASJ AF: 0.320

Gnomad4 EAS AF: 0.365

Gnomad4 SAS AF: 0.424

Gnomad4 FIN AF: 0.366

Gnomad4 NFE AF: 0.315

Gnomad4 OTH AF: 0.318

Alfa AF: 0.318 Hom.: 10924

Bravo AF: 0.250

Asia WGS AF: 0.365 AC: 1266 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	8.5
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: rs6946733; hg19: chr7-106670288;