6-30087866-G-T

Variant names:

• chr6-30087866-G-T
• rs6909253

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 0.612 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
• Publications: 34 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.687 AC: 28470 AN: 41430

American (AMR) AF: 0.608 AC: 9295 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.667 AC: 2315 AN: 3472

East Asian (EAS) AF: 0.491 AC: 2540 AN: 5168

South Asian (SAS) AF: 0.626 AC: 3019 AN: 4822

European-Finnish (FIN) AF: 0.532 AC: 5603 AN: 10540

Middle Eastern (MID) AF: 0.666 AC: 193 AN: 290

European-Non Finnish (NFE) AF: 0.584 AC: 39714 AN: 68002

Other (OTH) AF: 0.635 AC: 1342 AN: 2112

Alfa AF: 0.593 Hom.: 84861

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
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs6909253; hg19: chr6-30055643;