chr6-27777959-G-A

Variant names:

• chr6-27777959-G-A
• rs9461407

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 136,340 control chromosomes in the GnomAD database, including 7,540 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 (7540 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.67
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.501 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: 41618 AN: 136320 Hom.: 7532 Cov.: 25

Gnomad AFR AF: 0.507

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.202

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.305 AC: 41645 AN: 136340 Hom.: 7540 Cov.: 25 AF XY: 0.301 AC XY: 19619 AN XY: 65106

African (AFR) AF: 0.507 AC: 18599 AN: 36676

American (AMR) AF: 0.263 AC: 3354 AN: 12732

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 451 AN: 3354

East Asian (EAS) AF: 0.189 AC: 821 AN: 4354

South Asian (SAS) AF: 0.246 AC: 1014 AN: 4122

European-Finnish (FIN) AF: 0.153 AC: 1059 AN: 6912

Middle Eastern (MID) AF: 0.205 AC: 53 AN: 258

European-Non Finnish (NFE) AF: 0.237 AC: 15410 AN: 65146

Other (OTH) AF: 0.283 AC: 539 AN: 1902

Alfa AF: 0.227 Hom.: 1062

Bravo AF: 0.327

Asia WGS AF: 0.204 AC: 680 AN: 3322

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	0.0020
DANN	Benign	0.42
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs9461407; hg19: chr6-27745738; COSMIC: COSV68925849;