rs9890008

Variant names:

• chr17-14568376-A-G
• rs9890008
• ENST00000791247.1:n.322-4234T>C

Your query was ambiguous. Multiple possible variants found:

• chr17-14568376-A-G
• chr17-14568376-A-T

Variant summary

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

The ENST00000791247.1(ENSG00000303027):​n.322-4234T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.727 in 152,072 control chromosomes in the GnomAD database, including 40,379 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 0.73 (40379 hom., cov: 32)
• Consequence: ENSG00000303027 ENST00000791247.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0350
• Publications: 7 publications found

Genes affected

ENSG00000303027 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.781 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
ENSG00000303027	ENST00000791247.1	n.322-4234T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.727 AC: 110436 AN: 151952 Hom.: 40360 Cov.: 32

Gnomad AFR AF: 0.712

Gnomad AMI AF: 0.781

Gnomad AMR AF: 0.793

Gnomad ASJ AF: 0.662

Gnomad EAS AF: 0.630

Gnomad SAS AF: 0.611

Gnomad FIN AF: 0.688

Gnomad MID AF: 0.742

Gnomad NFE AF: 0.745

Gnomad OTH AF: 0.736

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

GnomAD4 genome AF: 0.727 AC: 110504 AN: 152072 Hom.: 40379 Cov.: 32 AF XY: 0.722 AC XY: 53654 AN XY: 74320

African (AFR) AF: 0.711 AC: 29512 AN: 41488

American (AMR) AF: 0.792 AC: 12115 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.662 AC: 2299 AN: 3472

East Asian (EAS) AF: 0.631 AC: 3247 AN: 5142

South Asian (SAS) AF: 0.610 AC: 2935 AN: 4808

European-Finnish (FIN) AF: 0.688 AC: 7280 AN: 10578

Middle Eastern (MID) AF: 0.733 AC: 214 AN: 292

European-Non Finnish (NFE) AF: 0.745 AC: 50641 AN: 67988

Other (OTH) AF: 0.736 AC: 1549 AN: 2104

Alfa AF: 0.734 Hom.: 23060

Bravo AF: 0.740

Asia WGS AF: 0.633 AC: 2204 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.8
DANN	Benign	0.56
PhyloP100		0.035

Splicing

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

Other links and lift over

dbSNP: rs9890008; hg19: chr17-14471693;