rs6946733

chr7-107029843-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;