6-30698892-C-G

Position:

• chr6-30698892-C-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.0486 in 152,076 control chromosomes in the GnomAD database, including 356 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 0.049 (356 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.30698892C>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0485 AC: 7377 AN: 151954 Hom.: 356 Cov.: 31

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.00991

Gnomad AMR AF: 0.0466

Gnomad ASJ AF: 0.0588

Gnomad EAS AF: 0.0613

Gnomad SAS AF: 0.0250

Gnomad FIN AF: 0.00690

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0143

Gnomad OTH AF: 0.0593

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

GnomAD4 genome AF: 0.0486 AC: 7384 AN: 152076 Hom.: 356 Cov.: 31 AF XY: 0.0480 AC XY: 3567 AN XY: 74334

Gnomad4 AFR AF: 0.116

Gnomad4 AMR AF: 0.0467

Gnomad4 ASJ AF: 0.0588

Gnomad4 EAS AF: 0.0614

Gnomad4 SAS AF: 0.0246

Gnomad4 FIN AF: 0.00690

Gnomad4 NFE AF: 0.0143

Gnomad4 OTH AF: 0.0582

Alfa AF: 0.00468 Hom.: 2

Bravo AF: 0.0563

Asia WGS AF: 0.0420 AC: 145 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
CADD	Benign	0.40
DANN	Benign	0.95

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9468811; hg19: chr6-30666669;