9-104175615-G-T

Variant names:

• chr9-104175615-G-T
• rs1450686
• ENST00000745188.1:n.710+28293C>A

Variant summary

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

The ENST00000745188.1(ENSG00000297079):​n.710+28293C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 151,988 control chromosomes in the GnomAD database, including 1,398 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 0.12 (1398 hom., cov: 32)
• Consequence: ENSG00000297079 ENST00000745188.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.211
• Publications: 2 publications found

Genes affected

ENSG00000297079 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.148 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000745188.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297079	ENST00000745188.1		n.710+28293C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18513 AN: 151870 Hom.: 1397 Cov.: 32

Gnomad AFR AF: 0.0717

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.0754

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.0276

Gnomad SAS AF: 0.0867

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.122 AC: 18531 AN: 151988 Hom.: 1398 Cov.: 32 AF XY: 0.123 AC XY: 9160 AN XY: 74304

African (AFR) AF: 0.0720 AC: 2987 AN: 41502

American (AMR) AF: 0.0752 AC: 1147 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 480 AN: 3464

East Asian (EAS) AF: 0.0277 AC: 143 AN: 5168

South Asian (SAS) AF: 0.0866 AC: 418 AN: 4828

European-Finnish (FIN) AF: 0.252 AC: 2655 AN: 10538

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10222 AN: 67932

Other (OTH) AF: 0.112 AC: 235 AN: 2106

Alfa AF: 0.0932 Hom.: 212

Bravo AF: 0.104

Asia WGS AF: 0.0490 AC: 170 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.5
DANN	Benign	0.68
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs1450686; hg19: chr9-106937896;