chr7-107029843-G-A

Variant names:

• chr7-107029843-G-A
• rs6946733

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0669 AC: 2778 AN: 41530

American (AMR) AF: 0.380 AC: 5801 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.320 AC: 1112 AN: 3472

East Asian (EAS) AF: 0.365 AC: 1886 AN: 5164

South Asian (SAS) AF: 0.424 AC: 2047 AN: 4826

European-Finnish (FIN) AF: 0.366 AC: 3858 AN: 10530

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.315 AC: 21416 AN: 67974

Other (OTH) AF: 0.318 AC: 670 AN: 2108

Alfa AF: 0.310 Hom.: 13272

Bravo AF: 0.250

Asia WGS AF: 0.365 AC: 1266 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	8.5
DANN	Benign	0.41
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs6946733; hg19: chr7-106670288;