6-93596534-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377899	XR_001744262.2	n.1450-32401A>G		intron_variant	Intron 3 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287683	ENST00000668367.1	n.213-69930A>G		intron_variant	Intron 2 of 4

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 v4.3

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

Other links and lift over

dbSNP: rs1906966; hg19: chr6-94306252;