rs17287745

Variant names:

• chr5-143275450-A-G
• rs17287745
• ENST00000770709.1:n.118-9249A>G

Variant summary

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

The ENST00000770709.1(ENSG00000300303):​n.118-9249A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.31 in 152,062 control chromosomes in the GnomAD database, including 8,397 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 (8397 hom., cov: 31)
• Consequence: ENSG00000300303 ENST00000770709.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.866
• Publications: 13 publications found

Genes affected

ENSG00000300303 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.405 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000770709.1. 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
	ENSG00000300303	ENST00000770709.1		n.118-9249A>G		intron	N/A
	ENSG00000300303	ENST00000770710.1		n.118-9249A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.310 AC: 47098 AN: 151946 Hom.: 8399 Cov.: 31

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.434

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.310 AC: 47096 AN: 152062 Hom.: 8397 Cov.: 31 AF XY: 0.305 AC XY: 22633 AN XY: 74312

African (AFR) AF: 0.143 AC: 5939 AN: 41510

American (AMR) AF: 0.305 AC: 4652 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.434 AC: 1507 AN: 3470

East Asian (EAS) AF: 0.179 AC: 928 AN: 5180

South Asian (SAS) AF: 0.366 AC: 1762 AN: 4818

European-Finnish (FIN) AF: 0.310 AC: 3276 AN: 10552

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.409 AC: 27806 AN: 67958

Other (OTH) AF: 0.331 AC: 697 AN: 2108

Alfa AF: 0.376 Hom.: 15103

Bravo AF: 0.303

Asia WGS AF: 0.277 AC: 968 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.4
DANN	Benign	0.62
PhyloP100		0.87

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: rs17287745;

hg19: chr5-142655015;

COSMIC: COSV59429544;