rs6979285

Variant names:

• chr7-133229130-G-A
• rs6979285

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 0.161 in 152,140 control chromosomes in the GnomAD database, including 4,093 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 0.16 (4093 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.423 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: 0.161 AC: 24487 AN: 152022 Hom.: 4076 Cov.: 32

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.0966

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.0493

Gnomad SAS AF: 0.0341

Gnomad FIN AF: 0.0355

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0555

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.161 AC: 24539 AN: 152140 Hom.: 4093 Cov.: 32 AF XY: 0.156 AC XY: 11625 AN XY: 74390

Gnomad4 AFR AF: 0.428

Gnomad4 AMR AF: 0.0964

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.0494

Gnomad4 SAS AF: 0.0337

Gnomad4 FIN AF: 0.0355

Gnomad4 NFE AF: 0.0555

Gnomad4 OTH AF: 0.148

Alfa AF: 0.121 Hom.: 402

Bravo AF: 0.177

Asia WGS AF: 0.0640 AC: 222 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.75
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6979285; hg19: chr7-132913887;