9-107765071-A-T

Variant names:

• chr9-107765071-A-T
• rs2177433
• ENST00000776894.1:n.528+12520A>T

Variant summary

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

The ENST00000776894.1(ENSG00000301188):​n.528+12520A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.835 in 151,868 control chromosomes in the GnomAD database, including 53,565 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 0.83 (53565 hom., cov: 31)
• Consequence: ENSG00000301188 ENST00000776894.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.631
• Publications: 2 publications found

Genes affected

ENSG00000301188 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.952 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376208	XR_007061720.1	n.403+12520A>T		intron_variant	Intron 2 of 5
LOC105376208	XR_930228.2	n.255+12520A>T		intron_variant	Intron 2 of 4
LOC105376208	XR_930229.2	n.255+12520A>T		intron_variant	Intron 2 of 6
LOC105376209	XR_930230.3	n.139-3782T>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301188	ENST00000776894.1	n.528+12520A>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.835 AC: 126658 AN: 151752 Hom.: 53503 Cov.: 31

Gnomad AFR AF: 0.960

Gnomad AMI AF: 0.855

Gnomad AMR AF: 0.865

Gnomad ASJ AF: 0.860

Gnomad EAS AF: 0.896

Gnomad SAS AF: 0.879

Gnomad FIN AF: 0.716

Gnomad MID AF: 0.834

Gnomad NFE AF: 0.760

Gnomad OTH AF: 0.851

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

GnomAD4 genome AF: 0.835 AC: 126774 AN: 151868 Hom.: 53565 Cov.: 31 AF XY: 0.834 AC XY: 61883 AN XY: 74186

African (AFR) AF: 0.960 AC: 39829 AN: 41474

American (AMR) AF: 0.865 AC: 13199 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.860 AC: 2978 AN: 3464

East Asian (EAS) AF: 0.896 AC: 4620 AN: 5156

South Asian (SAS) AF: 0.880 AC: 4241 AN: 4822

European-Finnish (FIN) AF: 0.716 AC: 7481 AN: 10454

Middle Eastern (MID) AF: 0.839 AC: 245 AN: 292

European-Non Finnish (NFE) AF: 0.760 AC: 51623 AN: 67926

Other (OTH) AF: 0.843 AC: 1778 AN: 2110

Alfa AF: 0.605 Hom.: 1103

Bravo AF: 0.854

Asia WGS AF: 0.907 AC: 3153 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.51
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs2177433; hg19: chr9-110527352;