rs196670

Variant names:

• chr6-79403878-G-A
• rs196670

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 0.214 in 152,100 control chromosomes in the GnomAD database, including 4,166 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 0.21 (4166 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.567

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.353 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: 0.214 AC: 32545 AN: 151982 Hom.: 4163 Cov.: 32

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.0897

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.214 AC: 32560 AN: 152100 Hom.: 4166 Cov.: 32 AF XY: 0.205 AC XY: 15243 AN XY: 74352

Gnomad4 AFR AF: 0.358

Gnomad4 AMR AF: 0.167

Gnomad4 ASJ AF: 0.188

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.0897

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.219

Alfa AF: 0.186 Hom.: 2106

Bravo AF: 0.228

Asia WGS AF: 0.132 AC: 462 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.8
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs196670; hg19: chr6-80113595;