rs6958059

Variant names:

• chr7-97092729-A-G
• rs6958059

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 0.419 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.418 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

Gnomad4 AFR AF: 0.515

Gnomad4 AMR AF: 0.391

Gnomad4 ASJ AF: 0.423

Gnomad4 EAS AF: 0.503

Gnomad4 SAS AF: 0.391

Gnomad4 FIN AF: 0.367

Gnomad4 NFE AF: 0.370

Gnomad4 OTH AF: 0.426

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6958059; hg19: chr7-96722041;