6-30979732-A-T

Variant names:

• chr6-30979732-A-T
• rs3094084

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 0.108 in 152,072 control chromosomes in the GnomAD database, including 1,180 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 0.11 (1180 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.753
• Publications: 16 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.16 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: 0.108 AC: 16460 AN: 151954 Hom.: 1180 Cov.: 31

Gnomad AFR AF: 0.0610

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.0599

Gnomad ASJ AF: 0.0619

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.00642

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.0895

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

GnomAD4 genome AF: 0.108 AC: 16463 AN: 152072 Hom.: 1180 Cov.: 31 AF XY: 0.102 AC XY: 7550 AN XY: 74354

African (AFR) AF: 0.0610 AC: 2531 AN: 41512

American (AMR) AF: 0.0598 AC: 914 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0619 AC: 215 AN: 3472

East Asian (EAS) AF: 0.00231 AC: 12 AN: 5190

South Asian (SAS) AF: 0.00622 AC: 30 AN: 4824

European-Finnish (FIN) AF: 0.126 AC: 1331 AN: 10524

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.162 AC: 11039 AN: 67942

Other (OTH) AF: 0.0885 AC: 187 AN: 2112

Alfa AF: 0.0904 Hom.: 156

Bravo AF: 0.104

Asia WGS AF: 0.0100 AC: 36 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	3.4
DANN	Benign	0.92
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs3094084; hg19: chr6-30947509;