rs6958059

Positions:

• chr7-97092729-A-G

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;