rs6976701

Variant names:

• chr7-128240560-G-A
• rs6976701

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;