chr6-30176643-C-A

Variant names:

• chr6-30176643-C-A
• rs2844786

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 0.303 in 151,884 control chromosomes in the GnomAD database, including 7,082 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 0.30 (7082 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.747
• Publications: 22 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.32 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: 0.303 AC: 46000 AN: 151766 Hom.: 7063 Cov.: 31

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.303 AC: 46065 AN: 151884 Hom.: 7082 Cov.: 31 AF XY: 0.302 AC XY: 22383 AN XY: 74228

African (AFR) AF: 0.324 AC: 13420 AN: 41376

American (AMR) AF: 0.324 AC: 4943 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 859 AN: 3470

East Asian (EAS) AF: 0.287 AC: 1485 AN: 5168

South Asian (SAS) AF: 0.187 AC: 903 AN: 4820

European-Finnish (FIN) AF: 0.307 AC: 3228 AN: 10528

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.298 AC: 20258 AN: 67940

Other (OTH) AF: 0.284 AC: 598 AN: 2104

Alfa AF: 0.298 Hom.: 7874

Bravo AF: 0.310

Asia WGS AF: 0.243 AC: 845 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.5
DANN	Benign	0.28
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs2844786; hg19: chr6-30144420;