9-17062836-G-A

Variant names:

• chr9-17062836-G-A
• rs914051
• ENST00000430545.4:n.393+13795G>A

Variant summary

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

The ENST00000430545.4(ENSG00000237153):​n.393+13795G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.432 in 151,968 control chromosomes in the GnomAD database, including 14,593 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 0.43 (14593 hom., cov: 32)
• Consequence: ENSG00000237153 ENST00000430545.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10

Genes affected

ENSG00000237153 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.484 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
ENSG00000237153	ENST00000430545.4	n.393+13795G>A		intron_variant	Intron 2 of 2	5
ENSG00000237153	ENST00000649821.1	n.179+9836G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.432 AC: 65616 AN: 151850 Hom.: 14566 Cov.: 32

Gnomad AFR AF: 0.489

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.442

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

GnomAD4 genome AF: 0.432 AC: 65689 AN: 151968 Hom.: 14593 Cov.: 32 AF XY: 0.418 AC XY: 31016 AN XY: 74262

African (AFR) AF: 0.490 AC: 20299 AN: 41434

American (AMR) AF: 0.361 AC: 5520 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.553 AC: 1918 AN: 3470

East Asian (EAS) AF: 0.307 AC: 1589 AN: 5174

South Asian (SAS) AF: 0.222 AC: 1070 AN: 4816

European-Finnish (FIN) AF: 0.311 AC: 3271 AN: 10516

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.449 AC: 30532 AN: 67950

Other (OTH) AF: 0.441 AC: 931 AN: 2110

Alfa AF: 0.439 Hom.: 1897

Bravo AF: 0.444

Asia WGS AF: 0.291 AC: 1011 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	5.9
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs914051; hg19: chr9-17062834;