9-108358415-T-G

Variant names:

• chr9-108358415-T-G
• rs10979327
• ENST00000826308.1:n.352+16927A>C

Variant summary

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

The ENST00000826308.1(ENSG00000307437):​n.352+16927A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.093 in 152,206 control chromosomes in the GnomAD database, including 1,246 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 0.093 (1246 hom., cov: 32)
• Consequence: ENSG00000307437 ENST00000826308.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.92
• Publications: 2 publications found

Genes affected

ENSG00000307437 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376214	XR_001746881.2	n.580+16927A>C		intron_variant	Intron 2 of 4
LOC105376214	XR_001746882.2	n.580+16927A>C		intron_variant	Intron 2 of 5
LOC105376214	XR_007061722.1	n.580+16927A>C		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000307437	ENST00000826308.1	n.352+16927A>C		intron_variant	Intron 2 of 3
ENSG00000307437	ENST00000826309.1	n.257+16927A>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0931 AC: 14156 AN: 152088 Hom.: 1241 Cov.: 32

Gnomad AFR AF: 0.0221

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.0636

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.467

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0986

Gnomad OTH AF: 0.0937

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

GnomAD4 genome AF: 0.0930 AC: 14157 AN: 152206 Hom.: 1246 Cov.: 32 AF XY: 0.0991 AC XY: 7376 AN XY: 74420

African (AFR) AF: 0.0221 AC: 917 AN: 41578

American (AMR) AF: 0.0635 AC: 971 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.106 AC: 368 AN: 3464

East Asian (EAS) AF: 0.467 AC: 2400 AN: 5142

South Asian (SAS) AF: 0.116 AC: 560 AN: 4824

European-Finnish (FIN) AF: 0.182 AC: 1929 AN: 10590

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0985 AC: 6700 AN: 67996

Other (OTH) AF: 0.101 AC: 214 AN: 2114

Alfa AF: 0.0885 Hom.: 1168

Bravo AF: 0.0819

Asia WGS AF: 0.264 AC: 916 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.23
DANN	Benign	0.66
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs10979327; hg19: chr9-111120695;