rs263580

Variant names:

• chr9-17039314-T-G
• rs263580
• ENST00000430545.4:n.271-9605T>G

Variant summary

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

The ENST00000649137.2(ENSG00000237153):​n.1591-9605T>G variant causes a intron 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: ENSG00000237153 ENST00000649137.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0250
• Publications: 5 publications found

Genes affected

ENSG00000237153 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000649137.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000237153	ENST00000430545.4	TSL:5	n.271-9605T>G		intron	N/A
	ENSG00000237153	ENST00000649137.2		n.1591-9605T>G		intron	N/A

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

African (AFR) AF: 0.562 AC: 23265 AN: 41432

American (AMR) AF: 0.493 AC: 7536 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.403 AC: 1398 AN: 3470

East Asian (EAS) AF: 0.553 AC: 2847 AN: 5144

South Asian (SAS) AF: 0.450 AC: 2164 AN: 4814

European-Finnish (FIN) AF: 0.417 AC: 4401 AN: 10558

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.453 AC: 30753 AN: 67936

Other (OTH) AF: 0.462 AC: 975 AN: 2110

Alfa AF: 0.460 Hom.: 8399

Bravo AF: 0.497

Asia WGS AF: 0.492 AC: 1705 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.1
DANN	Benign	0.81
PhyloP100		0.025

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs263580;

hg19: chr9-17039312;