chr6-90891816-G-A

Variant names:

• chr6-90891816-G-A
• rs12207515
• ENST00000828793.1:n.176-16240G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000828793.1(ENSG00000307789):​n.176-16240G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0923 in 151,202 control chromosomes in the GnomAD database, including 677 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 0.092 (677 hom., cov: 31)
• Consequence: ENSG00000307789 ENST00000828793.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.94
• Publications: 0 publications found

Genes affected

ENSG00000307789 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986623	XR_001744259.1	n.1244-16240G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000307789	ENST00000828793.1	n.176-16240G>A		intron_variant	Intron 1 of 3
ENSG00000307789	ENST00000828794.1	n.410+175G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0923 AC: 13947 AN: 151088 Hom.: 677 Cov.: 31

Gnomad AFR AF: 0.0853

Gnomad AMI AF: 0.0899

Gnomad AMR AF: 0.0698

Gnomad ASJ AF: 0.0932

Gnomad EAS AF: 0.00797

Gnomad SAS AF: 0.0884

Gnomad FIN AF: 0.0984

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.0923

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

GnomAD4 genome AF: 0.0923 AC: 13958 AN: 151202 Hom.: 677 Cov.: 31 AF XY: 0.0911 AC XY: 6723 AN XY: 73824

African (AFR) AF: 0.0855 AC: 3511 AN: 41060

American (AMR) AF: 0.0696 AC: 1057 AN: 15182

Ashkenazi Jewish (ASJ) AF: 0.0932 AC: 323 AN: 3464

East Asian (EAS) AF: 0.00779 AC: 40 AN: 5132

South Asian (SAS) AF: 0.0881 AC: 419 AN: 4756

European-Finnish (FIN) AF: 0.0984 AC: 1027 AN: 10432

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7264 AN: 67868

Other (OTH) AF: 0.0928 AC: 195 AN: 2102

Alfa AF: 0.105 Hom.: 542

Bravo AF: 0.0874

Asia WGS AF: 0.0590 AC: 205 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	20
DANN	Benign	0.69
PhyloP100		2.9

Splicing

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

Other links and lift over

dbSNP: rs12207515; hg19: chr6-91601534;