rs6958059

Variant names:

• chr7-97092729-A-G
• rs6958059

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 0.419 in 152,000 control chromosomes in the GnomAD database, including 13,641 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 0.42 (13641 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.211
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.509 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63558 AN: 151884 Hom.: 13611 Cov.: 32

Gnomad AFR AF: 0.515

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.423

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.423

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

GnomAD4 genome AF: 0.419 AC: 63641 AN: 152000 Hom.: 13641 Cov.: 32 AF XY: 0.419 AC XY: 31106 AN XY: 74302

African (AFR) AF: 0.515 AC: 21345 AN: 41432

American (AMR) AF: 0.391 AC: 5972 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.423 AC: 1464 AN: 3464

East Asian (EAS) AF: 0.503 AC: 2594 AN: 5160

South Asian (SAS) AF: 0.391 AC: 1886 AN: 4820

European-Finnish (FIN) AF: 0.367 AC: 3878 AN: 10568

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.370 AC: 25156 AN: 67968

Other (OTH) AF: 0.426 AC: 897 AN: 2106

Alfa AF: 0.397 Hom.: 1524

Bravo AF: 0.428

Asia WGS AF: 0.468 AC: 1627 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.40
DANN	Benign	0.45
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs6958059; hg19: chr7-96722041;