6-27085363-T-C

Variant names:

• chr6-27085363-T-C
• rs6930508

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 0.515 in 152,066 control chromosomes in the GnomAD database, including 22,211 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 0.51 (22211 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.510
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.765 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: 0.515 AC: 78229 AN: 151948 Hom.: 22168 Cov.: 32

Gnomad AFR AF: 0.771

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.309

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.503

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

GnomAD4 genome AF: 0.515 AC: 78313 AN: 152066 Hom.: 22211 Cov.: 32 AF XY: 0.512 AC XY: 38038 AN XY: 74330

African (AFR) AF: 0.772 AC: 32028 AN: 41496

American (AMR) AF: 0.433 AC: 6616 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 1122 AN: 3468

East Asian (EAS) AF: 0.309 AC: 1598 AN: 5178

South Asian (SAS) AF: 0.391 AC: 1891 AN: 4832

European-Finnish (FIN) AF: 0.453 AC: 4787 AN: 10566

Middle Eastern (MID) AF: 0.497 AC: 145 AN: 292

European-Non Finnish (NFE) AF: 0.423 AC: 28734 AN: 67936

Other (OTH) AF: 0.499 AC: 1054 AN: 2112

Alfa AF: 0.471 Hom.: 5191

Bravo AF: 0.527

Asia WGS AF: 0.345 AC: 1194 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.57
DANN	Benign	0.39
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs6930508; hg19: chr6-27053142;