chr9-99318136-A-G

Variant names:

• chr9-99318136-A-G
• rs162201
• ENST00000726034.1:n.610-419A>G

Variant summary

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

The ENST00000726034.1(ENSG00000294793):​n.610-419A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.512 in 152,106 control chromosomes in the GnomAD database, including 20,221 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 0.51 (20221 hom., cov: 32)
• Consequence: ENSG00000294793 ENST00000726034.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.635
• Publications: 6 publications found

Genes affected

ENSG00000294793 (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 (EAS) allele frequency at 95% confidence interval = 0.721 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902231	XR_007061691.1	n.108-419A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294793	ENST00000726034.1	n.610-419A>G		intron_variant	Intron 2 of 2
ENSG00000294793	ENST00000726035.1	n.1338-419A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.512 AC: 77891 AN: 151988 Hom.: 20213 Cov.: 32

Gnomad AFR AF: 0.478

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.559

Gnomad ASJ AF: 0.554

Gnomad EAS AF: 0.740

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.531

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.512 AC: 77929 AN: 152106 Hom.: 20221 Cov.: 32 AF XY: 0.515 AC XY: 38280 AN XY: 74372

African (AFR) AF: 0.477 AC: 19796 AN: 41474

American (AMR) AF: 0.558 AC: 8541 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.554 AC: 1924 AN: 3470

East Asian (EAS) AF: 0.740 AC: 3828 AN: 5170

South Asian (SAS) AF: 0.495 AC: 2387 AN: 4824

European-Finnish (FIN) AF: 0.531 AC: 5616 AN: 10572

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.500 AC: 33964 AN: 67984

Other (OTH) AF: 0.547 AC: 1155 AN: 2112

Alfa AF: 0.506 Hom.: 5216

Bravo AF: 0.513

Asia WGS AF: 0.653 AC: 2266 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.72
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs162201; hg19: chr9-102080418; COSMIC: COSV60381385;