rs6979348

Variant names:

• chr7-82746056-C-T
• rs6979348

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 0.301 in 151,994 control chromosomes in the GnomAD database, including 7,183 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 (7183 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.394 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: 0.301 AC: 45692 AN: 151874 Hom.: 7170 Cov.: 32

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.301 AC: 45743 AN: 151994 Hom.: 7183 Cov.: 32 AF XY: 0.302 AC XY: 22464 AN XY: 74286

African (AFR) AF: 0.213 AC: 8827 AN: 41488

American (AMR) AF: 0.339 AC: 5181 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 957 AN: 3468

East Asian (EAS) AF: 0.409 AC: 2104 AN: 5144

South Asian (SAS) AF: 0.353 AC: 1697 AN: 4814

European-Finnish (FIN) AF: 0.356 AC: 3760 AN: 10552

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.328 AC: 22261 AN: 67922

Other (OTH) AF: 0.319 AC: 674 AN: 2116

Alfa AF: 0.322 Hom.: 20910

Bravo AF: 0.295

Asia WGS AF: 0.372 AC: 1293 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.55
DANN	Benign	0.60
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs6979348; hg19: chr7-82375372;