9-97406516-A-T

Variant names:

• chr9-97406516-A-T
• rs11793735
• ENST00000667253.1:n.52-1726T>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000667253.1(ENSG00000286375):​n.52-1726T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.31 in 152,130 control chromosomes in the GnomAD database, including 7,361 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 0.31 (7361 hom., cov: 32)
• Consequence: ENSG00000286375 ENST00000667253.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

Genes affected

ENSG00000286375 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.334 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
ENSG00000286375	ENST00000667253.1	n.52-1726T>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.310 AC: 47149 AN: 152010 Hom.: 7357 Cov.: 32

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.273

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.334

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.310 AC: 47173 AN: 152130 Hom.: 7361 Cov.: 32 AF XY: 0.308 AC XY: 22935 AN XY: 74360

Gnomad4 AFR AF: 0.339

Gnomad4 AMR AF: 0.274

Gnomad4 ASJ AF: 0.406

Gnomad4 EAS AF: 0.272

Gnomad4 SAS AF: 0.253

Gnomad4 FIN AF: 0.273

Gnomad4 NFE AF: 0.308

Gnomad4 OTH AF: 0.317

Alfa AF: 0.313 Hom.: 939

Bravo AF: 0.312

Asia WGS AF: 0.268 AC: 938 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.77
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11793735; hg19: chr9-100168798;