rs7023003

Positions:

• chr9-105118389-A-G

Variant summary

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

The ENST00000666856.1(ENSG00000286536):​n.1857+49231T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 151,742 control chromosomes in the GnomAD database, including 7,079 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 0.28 (7079 hom., cov: 31)
• Consequence: ENST00000666856.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105376197	XR_930205.3	n.177-342A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000666856.1	n.1857+49231T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42392 AN: 151626 Hom.: 7050 Cov.: 31

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.280 AC: 42469 AN: 151742 Hom.: 7079 Cov.: 31 AF XY: 0.278 AC XY: 20585 AN XY: 74150

Gnomad4 AFR AF: 0.472

Gnomad4 AMR AF: 0.190

Gnomad4 ASJ AF: 0.207

Gnomad4 EAS AF: 0.313

Gnomad4 SAS AF: 0.192

Gnomad4 FIN AF: 0.221

Gnomad4 NFE AF: 0.203

Gnomad4 OTH AF: 0.261

Alfa AF: 0.237 Hom.: 868

Bravo AF: 0.289

Asia WGS AF: 0.266 AC: 923 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.79
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7023003; hg19: chr9-107880670;