6-169784287-A-G

Variant names:

• chr6-169784287-A-G
• rs7739088

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 0.305 in 152,060 control chromosomes in the GnomAD database, including 8,252 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 0.31 (8252 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.207
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.305 AC: 46306 AN: 151940 Hom.: 8216 Cov.: 33

Gnomad AFR AF: 0.491

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.261

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.305 AC: 46408 AN: 152060 Hom.: 8252 Cov.: 33 AF XY: 0.301 AC XY: 22404 AN XY: 74312

African (AFR) AF: 0.491 AC: 20361 AN: 41444

American (AMR) AF: 0.276 AC: 4213 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.263 AC: 912 AN: 3468

East Asian (EAS) AF: 0.327 AC: 1683 AN: 5148

South Asian (SAS) AF: 0.296 AC: 1425 AN: 4812

European-Finnish (FIN) AF: 0.159 AC: 1687 AN: 10584

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.225 AC: 15293 AN: 68006

Other (OTH) AF: 0.303 AC: 640 AN: 2112

Alfa AF: 0.278 Hom.: 895

Bravo AF: 0.323

Asia WGS AF: 0.347 AC: 1206 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.6
DANN	Benign	0.49
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs7739088; hg19: chr6-170184383; COSMIC: COSV64647849;