6-30124930-G-T

Position:

• chr6-30124930-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 0.746 in 152,142 control chromosomes in the GnomAD database, including 42,597 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 0.75 (42597 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.285

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.862 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.30124930G>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.746 AC: 113439 AN: 152024 Hom.: 42559 Cov.: 32

Gnomad AFR AF: 0.692

Gnomad AMI AF: 0.828

Gnomad AMR AF: 0.772

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.884

Gnomad SAS AF: 0.780

Gnomad FIN AF: 0.846

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.748

Gnomad OTH AF: 0.713

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

GnomAD4 genome AF: 0.746 AC: 113534 AN: 152142 Hom.: 42597 Cov.: 32 AF XY: 0.750 AC XY: 55745 AN XY: 74372

Gnomad4 AFR AF: 0.692

Gnomad4 AMR AF: 0.772

Gnomad4 ASJ AF: 0.693

Gnomad4 EAS AF: 0.884

Gnomad4 SAS AF: 0.781

Gnomad4 FIN AF: 0.846

Gnomad4 NFE AF: 0.748

Gnomad4 OTH AF: 0.717

Alfa AF: 0.750 Hom.: 59727

Bravo AF: 0.735

Asia WGS AF: 0.842 AC: 2926 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.6
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1419675; hg19: chr6-30092707;