rs17604706

Variant names:

• chr5-30936726-C-T
• rs17604706
• ENST00000797583.1:n.122-31140G>A

Variant summary

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

The ENST00000797583.1(ENSG00000303861):​n.122-31140G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 151,942 control chromosomes in the GnomAD database, including 7,651 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 (7651 hom., cov: 33)
• Consequence: ENSG00000303861 ENST00000797583.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.306
• Publications: 1 publications found

Genes affected

ENSG00000303861 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000797583.1. 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
	ENSG00000303861	ENST00000797583.1		n.122-31140G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46482 AN: 151824 Hom.: 7648 Cov.: 33

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.306 AC: 46485 AN: 151942 Hom.: 7651 Cov.: 33 AF XY: 0.307 AC XY: 22792 AN XY: 74226

African (AFR) AF: 0.191 AC: 7899 AN: 41460

American (AMR) AF: 0.305 AC: 4661 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.348 AC: 1207 AN: 3468

East Asian (EAS) AF: 0.245 AC: 1266 AN: 5164

South Asian (SAS) AF: 0.302 AC: 1453 AN: 4816

European-Finnish (FIN) AF: 0.386 AC: 4065 AN: 10538

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.364 AC: 24738 AN: 67918

Other (OTH) AF: 0.326 AC: 689 AN: 2112

Alfa AF: 0.350 Hom.: 4748

Bravo AF: 0.292

Asia WGS AF: 0.272 AC: 944 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.1
DANN	Benign	0.67
PhyloP100		0.31

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: rs17604706;

hg19: chr5-30936833;