6-98597873-A-G

Variant names:

• chr6-98597873-A-G
• rs6929790

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 0.257 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.257 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

African (AFR) AF: 0.426 AC: 17636 AN: 41444

American (AMR) AF: 0.170 AC: 2599 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 523 AN: 3472

East Asian (EAS) AF: 0.238 AC: 1234 AN: 5188

South Asian (SAS) AF: 0.252 AC: 1214 AN: 4826

European-Finnish (FIN) AF: 0.219 AC: 2315 AN: 10576

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.190 AC: 12917 AN: 67994

Other (OTH) AF: 0.235 AC: 496 AN: 2110

Alfa AF: 0.211 Hom.: 10333

Bravo AF: 0.259

Asia WGS AF: 0.273 AC: 946 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.9
DANN	Benign	0.66
PhyloP100		0.28

Splicing

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

Other links and lift over

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