9-103417564-C-T

Variant names:

• chr9-103417564-C-T
• rs1591687
• ENST00000421507.2:n.110+12219G>A

Variant summary

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

The ENST00000421507.2(ENSG00000226566):​n.110+12219G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0786 in 151,838 control chromosomes in the GnomAD database, including 629 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 0.079 (629 hom., cov: 32)
• Consequence: ENSG00000226566 ENST00000421507.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145
• Publications: 0 publications found

Genes affected

ENSG00000226566 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.157 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
ENSG00000226566	ENST00000421507.2	n.110+12219G>A		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.0784 AC: 11893 AN: 151720 Hom.: 624 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.0814

Gnomad ASJ AF: 0.0514

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.0902

Gnomad FIN AF: 0.0300

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0426

Gnomad OTH AF: 0.0730

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

GnomAD4 genome AF: 0.0786 AC: 11927 AN: 151838 Hom.: 629 Cov.: 32 AF XY: 0.0789 AC XY: 5858 AN XY: 74206

African (AFR) AF: 0.140 AC: 5807 AN: 41416

American (AMR) AF: 0.0816 AC: 1244 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.0514 AC: 178 AN: 3466

East Asian (EAS) AF: 0.167 AC: 858 AN: 5150

South Asian (SAS) AF: 0.0903 AC: 435 AN: 4816

European-Finnish (FIN) AF: 0.0300 AC: 317 AN: 10556

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0426 AC: 2895 AN: 67886

Other (OTH) AF: 0.0713 AC: 150 AN: 2104

Alfa AF: 0.0542 Hom.: 133

Bravo AF: 0.0836

Asia WGS AF: 0.116 AC: 404 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.7
DANN	Benign	0.48
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs1591687; hg19: chr9-106179846;