rs1017783

Positions:

• chr9-22920665-G-A
• chr9-22920665-G-C
• chr9-22920665-G-T

Variant summary

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

The ENST00000640003.1(ENSG00000284418):​n.369-46346C>T 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 0.312 in 150,114 control chromosomes in the GnomAD database, including 8,583 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 0.31 (8583 hom., cov: 30)
• Consequence: ENST00000640003.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.344

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375990	XR_929515.2	n.5078-3161C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000640003.1	n.369-46346C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.312 AC: 46760 AN: 149998 Hom.: 8581 Cov.: 30

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.416

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.312 AC: 46766 AN: 150114 Hom.: 8583 Cov.: 30 AF XY: 0.317 AC XY: 23167 AN XY: 73196

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.421

Gnomad4 ASJ AF: 0.407

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.346

Gnomad4 FIN AF: 0.455

Gnomad4 NFE AF: 0.386

Gnomad4 OTH AF: 0.325

Alfa AF: 0.359 Hom.: 5547

Bravo AF: 0.298

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.46
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1017783; hg19: chr9-22920664;