chr6-30465834-A-G

Position:

• chr6-30465834-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000685067.1(ENSG00000288805):​n.386-861T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.88 in 152,176 control chromosomes in the GnomAD database, including 58,997 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 0.88 (58997 hom., cov: 31)
• Consequence: ENST00000685067.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0370

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.967 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000685067.1	n.386-861T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.880 AC: 133768 AN: 152058 Hom.: 58944 Cov.: 31

Gnomad AFR AF: 0.896

Gnomad AMI AF: 0.916

Gnomad AMR AF: 0.879

Gnomad ASJ AF: 0.922

Gnomad EAS AF: 0.990

Gnomad SAS AF: 0.951

Gnomad FIN AF: 0.895

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.851

Gnomad OTH AF: 0.878

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

GnomAD4 genome AF: 0.880 AC: 133878 AN: 152176 Hom.: 58997 Cov.: 31 AF XY: 0.881 AC XY: 65564 AN XY: 74394

Gnomad4 AFR AF: 0.896

Gnomad4 AMR AF: 0.879

Gnomad4 ASJ AF: 0.922

Gnomad4 EAS AF: 0.990

Gnomad4 SAS AF: 0.951

Gnomad4 FIN AF: 0.895

Gnomad4 NFE AF: 0.851

Gnomad4 OTH AF: 0.879

Alfa AF: 0.867 Hom.: 81636

Bravo AF: 0.880

Asia WGS AF: 0.963 AC: 3351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.8
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2524172; hg19: chr6-30433611;