rs6979348

Positions:

• chr7-82746056-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;