rs6979285

Variant names:

• chr7-133229130-G-A
• rs6979285

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.428 AC: 17748 AN: 41444

American (AMR) AF: 0.0964 AC: 1472 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 358 AN: 3470

East Asian (EAS) AF: 0.0494 AC: 256 AN: 5180

South Asian (SAS) AF: 0.0337 AC: 163 AN: 4830

European-Finnish (FIN) AF: 0.0355 AC: 377 AN: 10606

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0555 AC: 3775 AN: 68014

Other (OTH) AF: 0.148 AC: 313 AN: 2116

Alfa AF: 0.111 Hom.: 719

Bravo AF: 0.177

Asia WGS AF: 0.0640 AC: 222 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.75
DANN	Benign	0.58
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs6979285; hg19: chr7-132913887;