9-91506284-T-A

Variant names:

• chr9-91506284-T-A
• rs6479347
• ENST00000738483.1:n.232-2083A>T

Variant summary

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

The ENST00000738483.1(ENSG00000296355):​n.232-2083A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.374 in 152,082 control chromosomes in the GnomAD database, including 13,195 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 0.37 (13195 hom., cov: 32)
• Consequence: ENSG00000296355 ENST00000738483.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.271
• Publications: 4 publications found

Genes affected

ENSG00000296355 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.654 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
ENSG00000296355	ENST00000738483.1	n.232-2083A>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.374 AC: 56784 AN: 151964 Hom.: 13170 Cov.: 32

Gnomad AFR AF: 0.661

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.374 AC: 56850 AN: 152082 Hom.: 13195 Cov.: 32 AF XY: 0.366 AC XY: 27249 AN XY: 74364

African (AFR) AF: 0.661 AC: 27402 AN: 41458

American (AMR) AF: 0.264 AC: 4043 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.287 AC: 995 AN: 3472

East Asian (EAS) AF: 0.279 AC: 1444 AN: 5174

South Asian (SAS) AF: 0.299 AC: 1442 AN: 4822

European-Finnish (FIN) AF: 0.218 AC: 2301 AN: 10574

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.267 AC: 18153 AN: 67974

Other (OTH) AF: 0.342 AC: 721 AN: 2110

Alfa AF: 0.148 Hom.: 237

Bravo AF: 0.392

Asia WGS AF: 0.317 AC: 1106 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.1
DANN	Benign	0.39
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs6479347; hg19: chr9-94268566;