rs6979348

Variant names:

• chr7-82746056-C-T
• rs6979348

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 0.301 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.301 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

Gnomad4 AFR AF: 0.213

Gnomad4 AMR AF: 0.339

Gnomad4 ASJ AF: 0.276

Gnomad4 EAS AF: 0.409

Gnomad4 SAS AF: 0.353

Gnomad4 FIN AF: 0.356

Gnomad4 NFE AF: 0.328

Gnomad4 OTH AF: 0.319

Alfa AF: 0.323 Hom.: 7378

Bravo AF: 0.295

Asia WGS AF: 0.372 AC: 1293 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6979348; hg19: chr7-82375372;