6-24093912-A-G

Variant names:

• chr6-24093912-A-G
• rs2176933
• ENST00000810475.1:n.94-26526A>G

Variant summary

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

The ENST00000810475.1(ENSG00000305332):​n.94-26526A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.803 in 152,102 control chromosomes in the GnomAD database, including 50,388 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 0.80 (50388 hom., cov: 31)
• Consequence: ENSG00000305332 ENST00000810475.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.372
• Publications: 1 publications found

Genes affected

ENSG00000305332 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.893 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000305332	ENST00000810475.1	n.94-26526A>G		intron_variant	Intron 1 of 2
ENSG00000305347	ENST00000810528.1	n.139+12431T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.803 AC: 122012 AN: 151984 Hom.: 50373 Cov.: 31

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.987

Gnomad AMR AF: 0.848

Gnomad ASJ AF: 0.863

Gnomad EAS AF: 0.679

Gnomad SAS AF: 0.885

Gnomad FIN AF: 0.914

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.899

Gnomad OTH AF: 0.832

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

GnomAD4 genome AF: 0.803 AC: 122063 AN: 152102 Hom.: 50388 Cov.: 31 AF XY: 0.806 AC XY: 59963 AN XY: 74358

African (AFR) AF: 0.593 AC: 24595 AN: 41446

American (AMR) AF: 0.848 AC: 12965 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.863 AC: 2993 AN: 3470

East Asian (EAS) AF: 0.679 AC: 3495 AN: 5150

South Asian (SAS) AF: 0.886 AC: 4274 AN: 4824

European-Finnish (FIN) AF: 0.914 AC: 9682 AN: 10592

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.899 AC: 61157 AN: 68010

Other (OTH) AF: 0.827 AC: 1749 AN: 2114

Alfa AF: 0.876 Hom.: 29753

Bravo AF: 0.787

Asia WGS AF: 0.753 AC: 2621 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.1
DANN	Benign	0.86
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs2176933; hg19: chr6-24094140;