rs9469003

Variant names:

• chr6-31440051-T-C
• rs9469003
• ENST00000673857.1:n.63-23072T>C

Variant summary

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

The ENST00000673857.1(ENSG00000288587):​n.63-23072T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 151,732 control chromosomes in the GnomAD database, including 4,229 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 0.22 (4229 hom., cov: 32)
• Consequence: ENSG00000288587 ENST00000673857.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.965

Genes affected

ENSG00000288587 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.309 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
ENSG00000288587	ENST00000673857.1	n.63-23072T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32747 AN: 151614 Hom.: 4221 Cov.: 32

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.220

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.216 AC: 32792 AN: 151732 Hom.: 4229 Cov.: 32 AF XY: 0.221 AC XY: 16402 AN XY: 74188

Gnomad4 AFR AF: 0.313

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.275

Gnomad4 EAS AF: 0.173

Gnomad4 SAS AF: 0.227

Gnomad4 FIN AF: 0.233

Gnomad4 NFE AF: 0.141

Gnomad4 OTH AF: 0.203

Alfa AF: 0.158 Hom.: 3686

Bravo AF: 0.222

Asia WGS AF: 0.197 AC: 684 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.9
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9469003; hg19: chr6-31407828;