6-30176643-C-A

Position:

• chr6-30176643-C-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;