6-30462705-G-C

Variant names:

• chr6-30462705-G-C
• rs2516676
• ENST00000685067.1:n.2079-189C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000685067.1(ENSG00000288805):​n.2079-189C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.859 in 152,176 control chromosomes in the GnomAD database, including 56,235 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 0.86 (56235 hom., cov: 31)
• Consequence: ENSG00000288805 ENST00000685067.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37
• Publications: 15 publications found

Genes affected

ENSG00000288805 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.923 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000685067.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000288805	ENST00000685067.1		n.2079-189C>G		intron	N/A
	ENSG00000288805	ENST00000765491.1		n.411-189C>G		intron	N/A
	ENSG00000288805	ENST00000765492.1		n.108-189C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.859 AC: 130618 AN: 152058 Hom.: 56185 Cov.: 31

Gnomad AFR AF: 0.855

Gnomad AMI AF: 0.916

Gnomad AMR AF: 0.860

Gnomad ASJ AF: 0.896

Gnomad EAS AF: 0.945

Gnomad SAS AF: 0.933

Gnomad FIN AF: 0.893

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.842

Gnomad OTH AF: 0.847

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

GnomAD4 genome AF: 0.859 AC: 130727 AN: 152176 Hom.: 56235 Cov.: 31 AF XY: 0.860 AC XY: 63989 AN XY: 74400

African (AFR) AF: 0.855 AC: 35455 AN: 41480

American (AMR) AF: 0.860 AC: 13161 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.896 AC: 3109 AN: 3470

East Asian (EAS) AF: 0.945 AC: 4900 AN: 5184

South Asian (SAS) AF: 0.933 AC: 4498 AN: 4820

European-Finnish (FIN) AF: 0.893 AC: 9457 AN: 10596

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.842 AC: 57269 AN: 68008

Other (OTH) AF: 0.849 AC: 1793 AN: 2112

Alfa AF: 0.853 Hom.: 27031

Bravo AF: 0.857

Asia WGS AF: 0.935 AC: 3250 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.62
DANN	Benign	0.37
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2516676; hg19: chr6-30430482;