6-100365312-G-A

Variant names:

• chr6-100365312-G-A
• rs1506084

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 0.36 in 151,972 control chromosomes in the GnomAD database, including 10,503 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 0.36 (10503 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0710
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.728 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: 0.360 AC: 54608 AN: 151854 Hom.: 10474 Cov.: 32

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.747

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.360 AC: 54687 AN: 151972 Hom.: 10503 Cov.: 32 AF XY: 0.364 AC XY: 27066 AN XY: 74282

African (AFR) AF: 0.263 AC: 10900 AN: 41450

American (AMR) AF: 0.434 AC: 6623 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.302 AC: 1045 AN: 3464

East Asian (EAS) AF: 0.748 AC: 3864 AN: 5168

South Asian (SAS) AF: 0.339 AC: 1631 AN: 4806

European-Finnish (FIN) AF: 0.409 AC: 4315 AN: 10550

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.370 AC: 25161 AN: 67964

Other (OTH) AF: 0.357 AC: 753 AN: 2108

Alfa AF: 0.355 Hom.: 16369

Bravo AF: 0.360

Asia WGS AF: 0.513 AC: 1779 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	12
DANN	Benign	0.79
PhyloP100		0.071

Splicing

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

Other links and lift over

dbSNP: rs1506084; hg19: chr6-100813188;