6-30087866-G-T

Position:

• chr6-30087866-G-T

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 0.612 in 152,026 control chromosomes in the GnomAD database, including 28,794 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 0.61 (28794 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.622

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.68 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.612 AC: 92991 AN: 151908 Hom.: 28750 Cov.: 32

Gnomad AFR AF: 0.687

Gnomad AMI AF: 0.653

Gnomad AMR AF: 0.608

Gnomad ASJ AF: 0.667

Gnomad EAS AF: 0.492

Gnomad SAS AF: 0.625

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.660

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.632

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

GnomAD4 genome AF: 0.612 AC: 93084 AN: 152026 Hom.: 28794 Cov.: 32 AF XY: 0.609 AC XY: 45236 AN XY: 74312

Gnomad4 AFR AF: 0.687

Gnomad4 AMR AF: 0.608

Gnomad4 ASJ AF: 0.667

Gnomad4 EAS AF: 0.491

Gnomad4 SAS AF: 0.626

Gnomad4 FIN AF: 0.532

Gnomad4 NFE AF: 0.584

Gnomad4 OTH AF: 0.635

Alfa AF: 0.585 Hom.: 29523

Bravo AF: 0.624

Asia WGS AF: 0.599 AC: 2085 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.5
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6909253; hg19: chr6-30055643;