9-90961551-C-T

Variant names:

• chr9-90961551-C-T
• rs426365
• ENST00000427745.1:n.130+3713G>A

Variant summary

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

The ENST00000427745.1(ENSG00000228216):​n.130+3713G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.982 in 152,310 control chromosomes in the GnomAD database, including 73,492 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 0.98 (73492 hom., cov: 33)
• Consequence: ENSG00000228216 ENST00000427745.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.76

Genes affected

ENSG00000228216 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.989 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105379829	XR_001746828.2	n.134+3713G>A		intron_variant	Intron 1 of 3
LOC105379829	XR_007061656.1	n.134+3713G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228216	ENST00000427745.1	n.130+3713G>A		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.982 AC: 149426 AN: 152192 Hom.: 73433 Cov.: 33

Gnomad AFR AF: 0.997

Gnomad AMI AF: 0.965

Gnomad AMR AF: 0.938

Gnomad ASJ AF: 0.990

Gnomad EAS AF: 0.901

Gnomad SAS AF: 0.907

Gnomad FIN AF: 0.996

Gnomad MID AF: 0.981

Gnomad NFE AF: 0.992

Gnomad OTH AF: 0.979

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

GnomAD4 genome AF: 0.982 AC: 149545 AN: 152310 Hom.: 73492 Cov.: 33 AF XY: 0.979 AC XY: 72912 AN XY: 74458

Gnomad4 AFR AF: 0.997

Gnomad4 AMR AF: 0.938

Gnomad4 ASJ AF: 0.990

Gnomad4 EAS AF: 0.901

Gnomad4 SAS AF: 0.908

Gnomad4 FIN AF: 0.996

Gnomad4 NFE AF: 0.992

Gnomad4 OTH AF: 0.980

Alfa AF: 0.986 Hom.: 92361

Bravo AF: 0.980

Asia WGS AF: 0.912 AC: 3171 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.41
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs426365; hg19: chr9-93723833;