rs9307613

Variant names:

• chr4-129436249-T-A
• rs9307613
• ENST00000723085.1:n.177+17225A>T

Your query was ambiguous. Multiple possible variants found:

• chr4-129436249-T-A
• chr4-129436249-T-C

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4 BA1

The ENST00000723085.1(ENSG00000287748):​n.177+17225A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.514 in 151,970 control chromosomes in the GnomAD database, including 22,746 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 0.51 (22746 hom., cov: 31)
• Consequence: ENSG00000287748 ENST00000723085.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.07
• Publications: 4 publications found

Genes affected

ENSG00000287748 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.1).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.794 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287748	ENST00000723085.1	n.177+17225A>T		intron_variant	Intron 1 of 2
ENSG00000287748	ENST00000723086.1	n.258-12832A>T		intron_variant	Intron 2 of 2
ENSG00000287748	ENST00000723087.1	n.495-12832A>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.514 AC: 77990 AN: 151852 Hom.: 22702 Cov.: 31

Gnomad AFR AF: 0.801

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.574

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.421

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.510

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

GnomAD4 genome AF: 0.514 AC: 78096 AN: 151970 Hom.: 22746 Cov.: 31 AF XY: 0.511 AC XY: 37932 AN XY: 74268

African (AFR) AF: 0.801 AC: 33232 AN: 41476

American (AMR) AF: 0.379 AC: 5777 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 1386 AN: 3468

East Asian (EAS) AF: 0.574 AC: 2958 AN: 5154

South Asian (SAS) AF: 0.388 AC: 1870 AN: 4818

European-Finnish (FIN) AF: 0.421 AC: 4447 AN: 10552

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.397 AC: 26939 AN: 67930

Other (OTH) AF: 0.512 AC: 1080 AN: 2110

Alfa AF: 0.313 Hom.: 796

Bravo AF: 0.524

Asia WGS AF: 0.523 AC: 1818 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.10
CADD	Benign	23
DANN	Benign	0.81
PhyloP100		3.1

Splicing

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

Other links and lift over

dbSNP: rs9307613; hg19: chr4-130357404;