6-30176643-C-A

Variant names:

• chr6-30176643-C-A
• rs2844786

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.324

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.248

Gnomad4 EAS AF: 0.287

Gnomad4 SAS AF: 0.187

Gnomad4 FIN AF: 0.307

Gnomad4 NFE AF: 0.298

Gnomad4 OTH AF: 0.284

Alfa AF: 0.297 Hom.: 4304

Bravo AF: 0.310

Asia WGS AF: 0.243 AC: 845 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2844786; hg19: chr6-30144420;