rs263580

Positions:

• chr9-17039314-T-G

Variant summary

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

The ENST00000649137.1(ENSG00000237153):​n.1591-9605T>G 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 0.486 in 151,950 control chromosomes in the GnomAD database, including 18,342 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 0.49 (18342 hom., cov: 32)
• Consequence: ENST00000649137.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0250

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.555 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375983	XR_001746628.1	n.226-9605T>G		intron_variant, non_coding_transcript_variant
LOC105375983	XR_001746629.2	n.468-9605T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000649137.1	n.1591-9605T>G		intron_variant, non_coding_transcript_variant
	ENST00000430545.4	n.271-9605T>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.486 AC: 73824 AN: 151832 Hom.: 18327 Cov.: 32

Gnomad AFR AF: 0.562

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.554

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.417

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.486 AC: 73875 AN: 151950 Hom.: 18342 Cov.: 32 AF XY: 0.481 AC XY: 35675 AN XY: 74244

Gnomad4 AFR AF: 0.562

Gnomad4 AMR AF: 0.493

Gnomad4 ASJ AF: 0.403

Gnomad4 EAS AF: 0.553

Gnomad4 SAS AF: 0.450

Gnomad4 FIN AF: 0.417

Gnomad4 NFE AF: 0.453

Gnomad4 OTH AF: 0.462

Alfa AF: 0.460 Hom.: 7569

Bravo AF: 0.497

Asia WGS AF: 0.492 AC: 1705 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.1
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs263580; hg19: chr9-17039312;