rs6945984

chr7-99750705-T-C

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 0.303 in 152,162 control chromosomes in the GnomAD database, including 12,139 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 0.30 (12139 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.267

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.698 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: 0.302 AC: 45951 AN: 152044 Hom.: 12100 Cov.: 32

Gnomad AFR AF: 0.704

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.276

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

GnomAD4 genome AF: 0.303 AC: 46050 AN: 152162 Hom.: 12139 Cov.: 32 AF XY: 0.303 AC XY: 22527 AN XY: 74416

Gnomad4 AFR AF: 0.705

Gnomad4 AMR AF: 0.259

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.299

Gnomad4 SAS AF: 0.350

Gnomad4 FIN AF: 0.109

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.277

Alfa AF: 0.176 Hom.: 1686

Bravo AF: 0.328

Asia WGS AF: 0.375 AC: 1303 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	5.2
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6945984; hg19: chr7-99348328;