rs6976701

chr7-128240560-G-A

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 0.0423 in 152,294 control chromosomes in the GnomAD database, including 311 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 0.042 (311 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0300

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.113 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: 0.0422 AC: 6428 AN: 152176 Hom.: 309 Cov.: 33

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.0384

Gnomad AMR AF: 0.0247

Gnomad ASJ AF: 0.0204

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0273

Gnomad FIN AF: 0.0220

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.00985

Gnomad OTH AF: 0.0378

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

GnomAD4 genome AF: 0.0423 AC: 6440 AN: 152294 Hom.: 311 Cov.: 33 AF XY: 0.0414 AC XY: 3086 AN XY: 74466

Gnomad4 AFR AF: 0.116

Gnomad4 AMR AF: 0.0246

Gnomad4 ASJ AF: 0.0204

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0271

Gnomad4 FIN AF: 0.0220

Gnomad4 NFE AF: 0.00985

Gnomad4 OTH AF: 0.0374

Alfa AF: 0.0334 Hom.: 33

Bravo AF: 0.0451

Asia WGS AF: 0.0220 AC: 78 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	3.0
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6976701; hg19: chr7-127880613;