6-39251827-G-C

Variant names:

• chr6-39251827-G-C
• rs1651105

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 0.415 in 152,008 control chromosomes in the GnomAD database, including 15,265 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 0.41 (15265 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.660
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.743 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: 0.415 AC: 62981 AN: 151890 Hom.: 15237 Cov.: 32

Gnomad AFR AF: 0.638

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.761

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.415 AC: 63066 AN: 152008 Hom.: 15265 Cov.: 32 AF XY: 0.422 AC XY: 31323 AN XY: 74308

African (AFR) AF: 0.638 AC: 26430 AN: 41434

American (AMR) AF: 0.411 AC: 6278 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.342 AC: 1186 AN: 3468

East Asian (EAS) AF: 0.762 AC: 3942 AN: 5170

South Asian (SAS) AF: 0.351 AC: 1695 AN: 4828

European-Finnish (FIN) AF: 0.358 AC: 3772 AN: 10548

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.273 AC: 18564 AN: 67968

Other (OTH) AF: 0.436 AC: 919 AN: 2108

Alfa AF: 0.341 Hom.: 1289

Bravo AF: 0.431

Asia WGS AF: 0.538 AC: 1870 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.24
DANN	Benign	0.53
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs1651105; hg19: chr6-39219603;