9-97406516-A-T

Variant names:

• chr9-97406516-A-T
• rs11793735
• ENST00000667253.2:n.65-1726T>A

Variant summary

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

The ENST00000667253.2(ENSG00000286375):​n.65-1726T>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 ENST00000667253.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 3 publications found

Genes affected

ENSG00000286375 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000667253.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286375	ENST00000667253.2		n.65-1726T>A		intron	N/A
	ENSG00000286375	ENST00000778879.1		n.58-4966T>A		intron	N/A

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

African (AFR) AF: 0.339 AC: 14071 AN: 41488

American (AMR) AF: 0.274 AC: 4190 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.406 AC: 1408 AN: 3472

East Asian (EAS) AF: 0.272 AC: 1413 AN: 5188

South Asian (SAS) AF: 0.253 AC: 1221 AN: 4822

European-Finnish (FIN) AF: 0.273 AC: 2889 AN: 10584

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.308 AC: 20912 AN: 67976

Other (OTH) AF: 0.317 AC: 668 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.77
DANN	Benign	0.25
PhyloP100		-1.0

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11793735;

hg19: chr9-100168798;