chr6-30804601-A-G

Position:

• chr6-30804601-A-G

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 0.854 in 152,168 control chromosomes in the GnomAD database, including 55,562 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 0.85 (55562 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.168

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.946 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.30804601A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00243	ENST00000419357.6	n.146-5829T>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.854 AC: 129777 AN: 152050 Hom.: 55514 Cov.: 32

Gnomad AFR AF: 0.838

Gnomad AMI AF: 0.906

Gnomad AMR AF: 0.863

Gnomad ASJ AF: 0.920

Gnomad EAS AF: 0.968

Gnomad SAS AF: 0.949

Gnomad FIN AF: 0.885

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.836

Gnomad OTH AF: 0.849

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

GnomAD4 genome AF: 0.854 AC: 129881 AN: 152168 Hom.: 55562 Cov.: 32 AF XY: 0.857 AC XY: 63766 AN XY: 74392

Gnomad4 AFR AF: 0.838

Gnomad4 AMR AF: 0.863

Gnomad4 ASJ AF: 0.920

Gnomad4 EAS AF: 0.968

Gnomad4 SAS AF: 0.948

Gnomad4 FIN AF: 0.885

Gnomad4 NFE AF: 0.836

Gnomad4 OTH AF: 0.850

Alfa AF: 0.849 Hom.: 82863

Bravo AF: 0.851

Asia WGS AF: 0.943 AC: 3281 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3094123; hg19: chr6-30772378;