chr6-93596534-A-G

Variant names:

• chr6-93596534-A-G
• rs1906966
• ENST00000668367.1:n.213-69930A>G

Variant summary

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

The ENST00000668367.1(ENSG00000287683):​n.213-69930A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.676 in 151,630 control chromosomes in the GnomAD database, including 34,841 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 0.68 (34841 hom., cov: 30)
• Consequence: ENSG00000287683 ENST00000668367.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.608
• Publications: 2 publications found

Genes affected

ENSG00000287683 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.738 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000668367.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287683	ENST00000668367.1		n.213-69930A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.676 AC: 102398 AN: 151512 Hom.: 34812 Cov.: 30

Gnomad AFR AF: 0.745

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.738

Gnomad EAS AF: 0.584

Gnomad SAS AF: 0.679

Gnomad FIN AF: 0.663

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.679

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

GnomAD4 genome AF: 0.676 AC: 102477 AN: 151630 Hom.: 34841 Cov.: 30 AF XY: 0.673 AC XY: 49898 AN XY: 74092

African (AFR) AF: 0.745 AC: 30831 AN: 41368

American (AMR) AF: 0.582 AC: 8828 AN: 15178

Ashkenazi Jewish (ASJ) AF: 0.738 AC: 2562 AN: 3470

East Asian (EAS) AF: 0.585 AC: 3005 AN: 5136

South Asian (SAS) AF: 0.677 AC: 3266 AN: 4822

European-Finnish (FIN) AF: 0.663 AC: 6987 AN: 10532

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.661 AC: 44789 AN: 67808

Other (OTH) AF: 0.678 AC: 1430 AN: 2110

Alfa AF: 0.651 Hom.: 14557

Bravo AF: 0.668

Asia WGS AF: 0.640 AC: 2223 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.77
DANN	Benign	0.23
PhyloP100		-0.61

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1906966;

hg19: chr6-94306252;