rs13287980

Variant names:

• chr9-104561919-G-A
• rs13287980
• ENST00000745188.1:n.371-31587C>T

Your query was ambiguous. Multiple possible variants found:

• chr9-104561919-G-A
• chr9-104561919-G-C
• chr9-104561919-G-T

Variant summary

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

The ENST00000745188.1(ENSG00000297079):​n.371-31587C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 152,098 control chromosomes in the GnomAD database, including 5,646 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 0.24 (5646 hom., cov: 33)
• Consequence: ENSG00000297079 ENST00000745188.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.194
• Publications: 6 publications found

Genes affected

ENSG00000297079 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000745188.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297079	ENST00000745188.1		n.371-31587C>T		intron	N/A
	ENSG00000297079	ENST00000745189.1		n.327-5401C>T		intron	N/A
	ENSG00000297079	ENST00000745190.1		n.349-5401C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35832 AN: 151980 Hom.: 5630 Cov.: 33

Gnomad AFR AF: 0.455

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.306

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.236 AC: 35904 AN: 152098 Hom.: 5646 Cov.: 33 AF XY: 0.237 AC XY: 17593 AN XY: 74358

African (AFR) AF: 0.455 AC: 18862 AN: 41470

American (AMR) AF: 0.160 AC: 2450 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 616 AN: 3466

East Asian (EAS) AF: 0.306 AC: 1586 AN: 5178

South Asian (SAS) AF: 0.270 AC: 1301 AN: 4824

European-Finnish (FIN) AF: 0.137 AC: 1445 AN: 10562

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.132 AC: 8987 AN: 67998

Other (OTH) AF: 0.221 AC: 468 AN: 2114

Alfa AF: 0.177 Hom.: 8871

Bravo AF: 0.245

Asia WGS AF: 0.275 AC: 953 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.1
DANN	Benign	0.36
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs13287980; hg19: chr9-107324200;