rs6929790

Variant names:

• chr6-98597873-A-G
• rs6929790

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 0.257 in 152,110 control chromosomes in the GnomAD database, including 5,949 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 0.26 (5949 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.279

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.42 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: 0.257 AC: 39128 AN: 151992 Hom.: 5938 Cov.: 32

Gnomad AFR AF: 0.426

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.257 AC: 39157 AN: 152110 Hom.: 5949 Cov.: 32 AF XY: 0.257 AC XY: 19101 AN XY: 74364

Gnomad4 AFR AF: 0.426

Gnomad4 AMR AF: 0.170

Gnomad4 ASJ AF: 0.151

Gnomad4 EAS AF: 0.238

Gnomad4 SAS AF: 0.252

Gnomad4 FIN AF: 0.219

Gnomad4 NFE AF: 0.190

Gnomad4 OTH AF: 0.235

Alfa AF: 0.199 Hom.: 5474

Bravo AF: 0.259

Asia WGS AF: 0.273 AC: 946 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.9
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6929790; hg19: chr6-99045749; COSMIC: COSV50465453;