rs9325776

Variant names:

• chr8-15960047-G-A
• rs9325776
• ENST00000664439.1:n.163+5298C>T

Your query was ambiguous. Multiple possible variants found:

• chr8-15960047-G-A
• chr8-15960047-G-C

Variant summary

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

The ENST00000664439.1(ENSG00000287476):​n.163+5298C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.943 in 152,180 control chromosomes in the GnomAD database, including 67,985 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 0.94 (67985 hom., cov: 33)
• Consequence: ENSG00000287476 ENST00000664439.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.578
• Publications: 0 publications found

Genes affected

ENSG00000287476 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.984 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
ENSG00000287476	ENST00000664439.1	n.163+5298C>T		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.943 AC: 143425 AN: 152062 Hom.: 67949 Cov.: 33

Gnomad AFR AF: 0.881

Gnomad AMI AF: 0.987

Gnomad AMR AF: 0.888

Gnomad ASJ AF: 0.999

Gnomad EAS AF: 0.851

Gnomad SAS AF: 0.924

Gnomad FIN AF: 0.991

Gnomad MID AF: 0.984

Gnomad NFE AF: 0.990

Gnomad OTH AF: 0.952

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

GnomAD4 genome AF: 0.943 AC: 143511 AN: 152180 Hom.: 67985 Cov.: 33 AF XY: 0.942 AC XY: 70085 AN XY: 74400

African (AFR) AF: 0.880 AC: 36479 AN: 41434

American (AMR) AF: 0.888 AC: 13586 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.999 AC: 3468 AN: 3470

East Asian (EAS) AF: 0.851 AC: 4402 AN: 5174

South Asian (SAS) AF: 0.924 AC: 4463 AN: 4828

European-Finnish (FIN) AF: 0.991 AC: 10528 AN: 10622

Middle Eastern (MID) AF: 0.983 AC: 289 AN: 294

European-Non Finnish (NFE) AF: 0.990 AC: 67381 AN: 68038

Other (OTH) AF: 0.952 AC: 2015 AN: 2116

Alfa AF: 0.948 Hom.: 23600

Bravo AF: 0.930

Asia WGS AF: 0.892 AC: 3098 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.66
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs9325776; hg19: chr8-15817556;